
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/GBM-TP/4432598/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/GBM-TP/4432582/GBM-TP.transferedmergedcluster.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=GBM-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=GBM-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=582, in cluster file=561, common to both=561
[1] "Reduce the number of clustering variables from 80 to 79."
[1]  79 561
[1] "1p gain"
[1] 3
      1P GAIN CNV 1P GAIN WILD-TYPE 
               39               522 
      1P GAIN CNV 1P GAIN WILD-TYPE 
               39               522 
[1] "1q gain"
[1] 3
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
               44               517 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
               44               517 
[1] "2p gain"
[1] 3
      2P GAIN CNV 2P GAIN WILD-TYPE 
               19               542 
      2P GAIN CNV 2P GAIN WILD-TYPE 
               19               542 
[1] "2q gain"
[1] 3
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
               17               544 
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
               17               544 
[1] "3p gain"
[1] 3
      3P GAIN CNV 3P GAIN WILD-TYPE 
               30               531 
      3P GAIN CNV 3P GAIN WILD-TYPE 
               30               531 
[1] "3q gain"
[1] 3
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               30               531 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               30               531 
[1] "4p gain"
[1] 3
      4P GAIN CNV 4P GAIN WILD-TYPE 
               15               546 
      4P GAIN CNV 4P GAIN WILD-TYPE 
               15               546 
[1] "4q gain"
[1] 3
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
               14               547 
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
               14               547 
[1] "5p gain"
[1] 3
      5P GAIN CNV 5P GAIN WILD-TYPE 
               30               531 
      5P GAIN CNV 5P GAIN WILD-TYPE 
               30               531 
[1] "5q gain"
[1] 3
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
               23               538 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
               23               538 
[1] "6p gain"
[1] 3
      6P GAIN CNV 6P GAIN WILD-TYPE 
                7               554 
      6P GAIN CNV 6P GAIN WILD-TYPE 
                7               554 
[1] "6q gain"
[1] 3
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                9               552 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                9               552 
[1] "7p gain"
[1] 3
      7P GAIN CNV 7P GAIN WILD-TYPE 
              431               130 
      7P GAIN CNV 7P GAIN WILD-TYPE 
              431               130 
[1] "7q gain"
[1] 3
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
              436               125 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
              436               125 
[1] "8p gain"
[1] 3
      8P GAIN CNV 8P GAIN WILD-TYPE 
               26               535 
      8P GAIN CNV 8P GAIN WILD-TYPE 
               26               535 
[1] "8q gain"
[1] 3
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               31               530 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               31               530 
[1] "9p gain"
[1] 3
      9P GAIN CNV 9P GAIN WILD-TYPE 
               17               544 
      9P GAIN CNV 9P GAIN WILD-TYPE 
               17               544 
[1] "9q gain"
[1] 3
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
               33               528 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
               33               528 
[1] "10p gain"
[1] 3
      10P GAIN CNV 10P GAIN WILD-TYPE 
                11                550 
      10P GAIN CNV 10P GAIN WILD-TYPE 
                11                550 
[1] "11p gain"
[1] 3
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 4                557 
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 4                557 
[1] "11q gain"
[1] 3
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 7                554 
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 7                554 
[1] "12p gain"
[1] 3
      12P GAIN CNV 12P GAIN WILD-TYPE 
                42                519 
      12P GAIN CNV 12P GAIN WILD-TYPE 
                42                519 
[1] "12q gain"
[1] 3
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                32                529 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                32                529 
[1] "13q gain"
[1] 3
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                 3                558 
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                 3                558 
[1] "14q gain"
[1] 3
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 7                554 
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 7                554 
[1] "15q gain"
[1] 3
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 6                555 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 6                555 
[1] "16p gain"
[1] 3
      16P GAIN CNV 16P GAIN WILD-TYPE 
                17                544 
      16P GAIN CNV 16P GAIN WILD-TYPE 
                17                544 
[1] "16q gain"
[1] 3
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                17                544 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                17                544 
[1] "17p gain"
[1] 3
      17P GAIN CNV 17P GAIN WILD-TYPE 
                11                550 
      17P GAIN CNV 17P GAIN WILD-TYPE 
                11                550 
[1] "17q gain"
[1] 3
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                19                542 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                19                542 
[1] "18p gain"
[1] 3
      18P GAIN CNV 18P GAIN WILD-TYPE 
                27                534 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                27                534 
[1] "18q gain"
[1] 3
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                29                532 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                29                532 
[1] "19p gain"
[1] 3
      19P GAIN CNV 19P GAIN WILD-TYPE 
               176                385 
      19P GAIN CNV 19P GAIN WILD-TYPE 
               176                385 
[1] "19q gain"
[1] 3
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
               151                410 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
               151                410 
[1] "20p gain"
[1] 3
      20P GAIN CNV 20P GAIN WILD-TYPE 
               180                381 
      20P GAIN CNV 20P GAIN WILD-TYPE 
               180                381 
[1] "20q gain"
[1] 3
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
               178                383 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
               178                383 
[1] "21q gain"
[1] 3
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                35                526 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                35                526 
[1] "22q gain"
[1] 3
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                11                550 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                11                550 
[1] "Xq gain"
[1] 3
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                3               558 
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                3               558 
[1] "1p loss"
[1] 3
      1P LOSS CNV 1P LOSS WILD-TYPE 
                5               556 
      1P LOSS CNV 1P LOSS WILD-TYPE 
                5               556 
[1] "1q loss"
[1] 3
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                4               557 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                4               557 
[1] "2p loss"
[1] 3
      2P LOSS CNV 2P LOSS WILD-TYPE 
               10               551 
      2P LOSS CNV 2P LOSS WILD-TYPE 
               10               551 
[1] "2q loss"
[1] 3
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                9               552 
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                9               552 
[1] "3p loss"
[1] 3
      3P LOSS CNV 3P LOSS WILD-TYPE 
               22               539 
      3P LOSS CNV 3P LOSS WILD-TYPE 
               22               539 
[1] "3q loss"
[1] 3
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
               16               545 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
               16               545 
[1] "4p loss"
[1] 3
      4P LOSS CNV 4P LOSS WILD-TYPE 
               26               535 
      4P LOSS CNV 4P LOSS WILD-TYPE 
               26               535 
[1] "4q loss"
[1] 3
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               25               536 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               25               536 
[1] "5p loss"
[1] 3
      5P LOSS CNV 5P LOSS WILD-TYPE 
               21               540 
      5P LOSS CNV 5P LOSS WILD-TYPE 
               21               540 
[1] "5q loss"
[1] 3
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
               20               541 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
               20               541 
[1] "6p loss"
[1] 3
      6P LOSS CNV 6P LOSS WILD-TYPE 
               46               515 
      6P LOSS CNV 6P LOSS WILD-TYPE 
               46               515 
[1] "6q loss"
[1] 3
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               80               481 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               80               481 
[1] "7p loss"
[1] 3
      7P LOSS CNV 7P LOSS WILD-TYPE 
                5               556 
      7P LOSS CNV 7P LOSS WILD-TYPE 
                5               556 
[1] "7q loss"
[1] 3
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
                4               557 
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
                4               557 
[1] "8p loss"
[1] 3
      8P LOSS CNV 8P LOSS WILD-TYPE 
               34               527 
      8P LOSS CNV 8P LOSS WILD-TYPE 
               34               527 
[1] "8q loss"
[1] 3
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
               21               540 
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
               21               540 
[1] "9p loss"
[1] 3
      9P LOSS CNV 9P LOSS WILD-TYPE 
              165               396 
      9P LOSS CNV 9P LOSS WILD-TYPE 
              165               396 
[1] "9q loss"
[1] 3
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
               64               497 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
               64               497 
[1] "10p loss"
[1] 3
      10P LOSS CNV 10P LOSS WILD-TYPE 
               434                127 
      10P LOSS CNV 10P LOSS WILD-TYPE 
               434                127 
[1] "10q loss"
[1] 3
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
               447                114 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
               447                114 
[1] "11p loss"
[1] 3
      11P LOSS CNV 11P LOSS WILD-TYPE 
                63                498 
      11P LOSS CNV 11P LOSS WILD-TYPE 
                63                498 
[1] "11q loss"
[1] 3
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                54                507 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                54                507 
[1] "12p loss"
[1] 3
      12P LOSS CNV 12P LOSS WILD-TYPE 
                38                523 
      12P LOSS CNV 12P LOSS WILD-TYPE 
                38                523 
[1] "12q loss"
[1] 3
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                35                526 
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                35                526 
[1] "13q loss"
[1] 3
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
               138                423 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
               138                423 
[1] "14q loss"
[1] 3
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
               120                441 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
               120                441 
[1] "15q loss"
[1] 3
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                62                499 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                62                499 
[1] "16p loss"
[1] 3
      16P LOSS CNV 16P LOSS WILD-TYPE 
                23                538 
      16P LOSS CNV 16P LOSS WILD-TYPE 
                23                538 
[1] "16q loss"
[1] 3
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                41                520 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                41                520 
[1] "17p loss"
[1] 3
      17P LOSS CNV 17P LOSS WILD-TYPE 
                36                525 
      17P LOSS CNV 17P LOSS WILD-TYPE 
                36                525 
[1] "17q loss"
[1] 3
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                19                542 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                19                542 
[1] "18p loss"
[1] 3
      18P LOSS CNV 18P LOSS WILD-TYPE 
                44                517 
      18P LOSS CNV 18P LOSS WILD-TYPE 
                44                517 
[1] "18q loss"
[1] 3
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                38                523 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                38                523 
[1] "19p loss"
[1] 3
      19P LOSS CNV 19P LOSS WILD-TYPE 
                12                549 
      19P LOSS CNV 19P LOSS WILD-TYPE 
                12                549 
[1] "19q loss"
[1] 3
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                16                545 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                16                545 
[1] "20p loss"
[1] 3
      20P LOSS CNV 20P LOSS WILD-TYPE 
                11                550 
      20P LOSS CNV 20P LOSS WILD-TYPE 
                11                550 
[1] "20q loss"
[1] 3
      20Q LOSS CNV 20Q LOSS WILD-TYPE 
                10                551 
      20Q LOSS CNV 20Q LOSS WILD-TYPE 
                10                551 
[1] "21q loss"
[1] 3
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                25                536 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                25                536 
[1] "22q loss"
[1] 3
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
               140                421 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
               140                421 
[1] "Xq loss"
[1] 3
      XQ LOSS CNV XQ LOSS WILD-TYPE 
               11               550 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
               11               550 
[1] "data2feature, selection="
 [1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "MIR_CNMF"             
 [4] "MIR_CHIERARCHICAL"     "CN_CNMF"               "METHLYATION_CNMF"     
 [7] "RPPA_CNMF"             "RPPA_CHIERARCHICAL"    "MRNASEQ_CNMF"         
[10] "MRNASEQ_CHIERARCHICAL"

Input Data has 10 rows and 561 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:'MIR_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MIR_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'METHLYATION_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RPPA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "MIR_CNMF"             
 [4] "MIR_CHIERARCHICAL"     "CN_CNMF"               "METHLYATION_CNMF"     
 [7] "RPPA_CNMF"             "RPPA_CHIERARCHICAL"    "MRNASEQ_CNMF"         
[10] "MRNASEQ_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 561 columns, 0 survival variables, and 10 non-survival variables.
MRNA_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIR_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIR_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=4, 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

Clustering(1) Variable = 1p gain
D1V1, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1          11               136
  CLUS_2           8                88
  CLUS_3           7               145
  CLUS_4           7               106
D1V2, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           4               113
  CLUS_2           9               162
  CLUS_3          20               200
D1V3, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1          10               129
  CLUS_2          12               143
  CLUS_3           4                69
  CLUS_4           8                96
D1V4, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1          19               162
  CLUS_2           7               148
  CLUS_3           8               127
D1V5, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1          24               137
  CLUS_2           9               179
  CLUS_3           6               206
D1V6, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           4                35
  CLUS_2           1                26
  CLUS_3           0                16
  CLUS_4           1                26
D1V7, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           3                51
  CLUS_2           2                56
  CLUS_3           3                41
  CLUS_4           5                40
D1V8, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           5                59
  CLUS_2           2                31
  CLUS_3           6                98
D1V9, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           2                42
  CLUS_2           8                59
  CLUS_3           3                33
D1V10, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           7                59
  CLUS_2           4                17
  CLUS_3           2                58

Clustering(2) Variable = 1q gain
D2V1, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          11               136
  CLUS_2          14                82
  CLUS_3           7               145
  CLUS_4           6               107
D2V2, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           5               112
  CLUS_2          11               160
  CLUS_3          22               198
D2V3, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           9               130
  CLUS_2          13               142
  CLUS_3           4                69
  CLUS_4          12                92
D2V4, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          18               163
  CLUS_2          10               145
  CLUS_3          10               125
D2V5, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          29               132
  CLUS_2          11               177
  CLUS_3           4               208
D2V6, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           5                34
  CLUS_2           1                26
  CLUS_3           0                16
  CLUS_4           2                25
D2V7, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           4                50
  CLUS_2           3                55
  CLUS_3           4                40
  CLUS_4           5                40
D2V8, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           6                58
  CLUS_2           2                31
  CLUS_3           8                96
D2V9, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           4                40
  CLUS_2           7                60
  CLUS_3           3                33
D2V10, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           7                59
  CLUS_2           4                17
  CLUS_3           3                57

Clustering(3) Variable = 2p gain
D3V1, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           5               142
  CLUS_2           6                90
  CLUS_3           2               150
  CLUS_4           4               109
D3V2, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           2               115
  CLUS_2           6               165
  CLUS_3           9               211
D3V3, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           5               134
  CLUS_2           2               153
  CLUS_3           0                73
  CLUS_4          10                94
D3V4, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           5               176
  CLUS_2          10               145
  CLUS_3           2               133
D3V5, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           8               153
  CLUS_2           6               182
  CLUS_3           5               207
D3V6, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           1                38
  CLUS_2           0                27
  CLUS_3           0                16
  CLUS_4           2                25
D3V7, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           1                53
  CLUS_2           2                56
  CLUS_3           2                42
  CLUS_4           3                42
D3V8, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           2                62
  CLUS_2           0                33
  CLUS_3           6                98
D3V9, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           2                42
  CLUS_2           2                65
  CLUS_3           0                36
D3V10, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           3                63
  CLUS_2           0                21
  CLUS_3           1                59

Clustering(4) Variable = 2q gain
D4V1, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           5               142
  CLUS_2           5                91
  CLUS_3           2               150
  CLUS_4           2               111
D4V2, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           2               115
  CLUS_2           3               168
  CLUS_3           9               211
D4V3, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           5               134
  CLUS_2           0               155
  CLUS_3           0                73
  CLUS_4          10                94
D4V4, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           3               178
  CLUS_2          10               145
  CLUS_3           2               133
D4V5, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           7               154
  CLUS_2           5               183
  CLUS_3           5               207
D4V6, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           1                38
  CLUS_2           0                27
  CLUS_3           0                16
  CLUS_4           2                25
D4V7, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           1                53
  CLUS_2           1                57
  CLUS_3           2                42
  CLUS_4           3                42
D4V8, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           2                62
  CLUS_2           0                33
  CLUS_3           5                99
D4V9, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           1                43
  CLUS_2           2                65
  CLUS_3           0                36
D4V10, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           3                63
  CLUS_2           0                21
  CLUS_3           0                60

Clustering(5) Variable = 3p gain
D5V1, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           9               138
  CLUS_2          10                86
  CLUS_3           2               150
  CLUS_4           7               106
D5V2, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           2               115
  CLUS_2          14               157
  CLUS_3          12               208
D5V3, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1          10               129
  CLUS_2           5               150
  CLUS_3           4                69
  CLUS_4           8                96
D5V4, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           8               173
  CLUS_2          10               145
  CLUS_3           9               126
D5V5, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1          14               147
  CLUS_2          11               177
  CLUS_3           5               207
D5V6, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           1                38
  CLUS_2           0                27
  CLUS_3           0                16
  CLUS_4           3                24
D5V7, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           2                52
  CLUS_2           2                56
  CLUS_3           0                44
  CLUS_4           3                42
D5V8, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           0                64
  CLUS_2           1                32
  CLUS_3           6                98
D5V9, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           3                41
  CLUS_2           4                63
  CLUS_3           1                35
D5V10, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           4                62
  CLUS_2           0                21
  CLUS_3           4                56

Clustering(6) Variable = 3q gain
D6V1, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           9               138
  CLUS_2          10                86
  CLUS_3           2               150
  CLUS_4           7               106
D6V2, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           2               115
  CLUS_2          14               157
  CLUS_3          12               208
D6V3, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1          10               129
  CLUS_2           5               150
  CLUS_3           4                69
  CLUS_4           8                96
D6V4, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           9               172
  CLUS_2           9               146
  CLUS_3           9               126
D6V5, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1          14               147
  CLUS_2          10               178
  CLUS_3           6               206
D6V6, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           1                38
  CLUS_2           0                27
  CLUS_3           0                16
  CLUS_4           3                24
D6V7, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           2                52
  CLUS_2           2                56
  CLUS_3           0                44
  CLUS_4           3                42
D6V8, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           0                64
  CLUS_2           1                32
  CLUS_3           6                98
D6V9, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           3                41
  CLUS_2           5                62
  CLUS_3           1                35
D6V10, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           5                61
  CLUS_2           0                21
  CLUS_3           4                56

Clustering(7) Variable = 4p gain
D7V1, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           3               144
  CLUS_2           6                90
  CLUS_3           5               147
  CLUS_4           0               113
D7V2, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           5               112
  CLUS_2           4               167
  CLUS_3           5               215
D7V3, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           6               133
  CLUS_2           6               149
  CLUS_3           1                72
  CLUS_4           1               103
D7V4, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           9               172
  CLUS_2           1               154
  CLUS_3           4               131
D7V5, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           3               158
  CLUS_2           8               180
  CLUS_3           4               208
D7V6, multiclass
[1] "Remove cluster labels:" "4P GAIN CNV"           
clus
      4P GAIN CNV 4P GAIN WILD-TYPE 
                1               108 
       TCGA-06-0650        TCGA-06-1804        TCGA-06-1806        TCGA-06-5408 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-06-6388 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-6389        TCGA-06-6390        TCGA-06-6391        TCGA-06-6693 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-6694        TCGA-06-6695        TCGA-06-6698        TCGA-06-6699 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-6700        TCGA-06-6701        TCGA-12-5295        TCGA-12-5299 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-12-5301        TCGA-14-0740        TCGA-14-0781        TCGA-14-0862 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-14-1043        TCGA-14-1395        TCGA-14-1450        TCGA-15-1444 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-19-4065        TCGA-19-5947        TCGA-19-5950        TCGA-19-5951 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-19-5952        TCGA-19-5953        TCGA-19-5954        TCGA-19-5955 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-19-5956        TCGA-19-5958        TCGA-19-5959        TCGA-19-5960 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-26-6173 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-26-6174        TCGA-28-2501        TCGA-28-2510        TCGA-28-5204 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-28-5207        TCGA-28-5208        TCGA-28-5209        TCGA-28-5211 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-28-5213        TCGA-28-5214        TCGA-28-5215        TCGA-28-5216 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5219        TCGA-28-5220        TCGA-28-6450 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-32-1979        TCGA-32-1980        TCGA-32-5222        TCGA-41-5651 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4925 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-76-4926        TCGA-76-4928        TCGA-76-4929        TCGA-76-4931 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-76-4934        TCGA-76-4935        TCGA-76-6191        TCGA-76-6192 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-76-6193        TCGA-76-6280        TCGA-76-6282        TCGA-76-6283 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-76-6285        TCGA-76-6286        TCGA-76-6656        TCGA-76-6657 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-76-6660        TCGA-76-6661        TCGA-76-6662        TCGA-76-6663 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-76-6664        TCGA-81-5910        TCGA-81-5911        TCGA-87-5896 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V7, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           3                51
  CLUS_2           1                57
  CLUS_3           0                44
  CLUS_4           1                44
D7V8, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           0                64
  CLUS_2           2                31
  CLUS_3           3               101
D7V9, multiclass
[1] "Remove cluster labels:" "4P GAIN CNV"           
clus
      4P GAIN CNV 4P GAIN WILD-TYPE 
                1               146 
       TCGA-02-0047        TCGA-02-0055        TCGA-02-2483        TCGA-02-2485 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-02-2486        TCGA-06-0125        TCGA-06-0129        TCGA-06-0130 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0132        TCGA-06-0138        TCGA-06-0141        TCGA-06-0157 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0158        TCGA-06-0168        TCGA-06-0178        TCGA-06-0184 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0187        TCGA-06-0190        TCGA-06-0210        TCGA-06-0211 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0219        TCGA-06-0238        TCGA-06-0644        TCGA-06-0645 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0646        TCGA-06-0649        TCGA-06-0686        TCGA-06-0743 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0744        TCGA-06-0745        TCGA-06-0747        TCGA-06-0749 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0750        TCGA-06-0878        TCGA-06-0882        TCGA-06-1804 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-2557        TCGA-06-2558        TCGA-06-2559        TCGA-06-2561 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-2562        TCGA-06-2563        TCGA-06-2564        TCGA-06-2565 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-2567        TCGA-06-2569        TCGA-06-2570        TCGA-06-5408 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-08-0386 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-12-0616        TCGA-12-0618        TCGA-12-0619        TCGA-12-0821 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-12-3650        TCGA-12-3652        TCGA-12-3653        TCGA-12-5295 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-12-5299        TCGA-14-0781        TCGA-14-0787        TCGA-14-0789 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-14-0790        TCGA-14-0817        TCGA-14-1034        TCGA-14-1823 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-14-1825        TCGA-14-1829        TCGA-14-2554        TCGA-15-0742 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-15-1444        TCGA-16-0846        TCGA-16-1045        TCGA-19-1390 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-19-1787        TCGA-19-2619        TCGA-19-2620        TCGA-19-2624 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-19-2625        TCGA-19-2629        TCGA-19-4065        TCGA-19-5960 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-27-1830 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-27-1831        TCGA-27-1832        TCGA-27-1834        TCGA-27-1835 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-27-1837        TCGA-27-2519        TCGA-27-2521        TCGA-27-2523 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-27-2524        TCGA-27-2526        TCGA-27-2528        TCGA-28-1747 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-28-1753        TCGA-28-2509        TCGA-28-2510        TCGA-28-2513 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-28-2514        TCGA-28-5204        TCGA-28-5207        TCGA-28-5208 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-28-5209        TCGA-28-5213        TCGA-28-5215        TCGA-28-5216 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5220        TCGA-32-1970        TCGA-32-1980 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-32-1982        TCGA-32-2615        TCGA-32-2616        TCGA-32-2632 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-32-2634        TCGA-32-2638        TCGA-32-4213        TCGA-32-5222 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-41-2571        TCGA-41-2572        TCGA-41-3915        TCGA-41-4097 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-41-5651        TCGA-76-4925        TCGA-76-4926        TCGA-76-4928 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-76-4929        TCGA-76-4931 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V10, multiclass
[1] "Remove cluster labels:" "4P GAIN CNV"           
clus
      4P GAIN CNV 4P GAIN WILD-TYPE 
                1               146 
       TCGA-02-0047        TCGA-02-0055        TCGA-02-2483        TCGA-02-2485 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-02-2486        TCGA-06-0125        TCGA-06-0129        TCGA-06-0130 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0132        TCGA-06-0138        TCGA-06-0141        TCGA-06-0157 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0158        TCGA-06-0168        TCGA-06-0178        TCGA-06-0184 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0187        TCGA-06-0190        TCGA-06-0210        TCGA-06-0211 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0219        TCGA-06-0238        TCGA-06-0644        TCGA-06-0645 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0646        TCGA-06-0649        TCGA-06-0686        TCGA-06-0743 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0744        TCGA-06-0745        TCGA-06-0747        TCGA-06-0749 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0750        TCGA-06-0878        TCGA-06-0882        TCGA-06-1804 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-2557        TCGA-06-2558        TCGA-06-2559        TCGA-06-2561 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-2562        TCGA-06-2563        TCGA-06-2564        TCGA-06-2565 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-2567        TCGA-06-2569        TCGA-06-2570        TCGA-06-5408 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-08-0386 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-12-0616        TCGA-12-0618        TCGA-12-0619        TCGA-12-0821 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-12-3650        TCGA-12-3652        TCGA-12-3653        TCGA-12-5295 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-12-5299        TCGA-14-0781        TCGA-14-0787        TCGA-14-0789 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-14-0790        TCGA-14-0817        TCGA-14-1034        TCGA-14-1823 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-14-1825        TCGA-14-1829        TCGA-14-2554        TCGA-15-0742 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-15-1444        TCGA-16-0846        TCGA-16-1045        TCGA-19-1390 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-19-1787        TCGA-19-2619        TCGA-19-2620        TCGA-19-2624 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-19-2625        TCGA-19-2629        TCGA-19-4065        TCGA-19-5960 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-27-1830 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-27-1831        TCGA-27-1832        TCGA-27-1834        TCGA-27-1835 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-27-1837        TCGA-27-2519        TCGA-27-2521        TCGA-27-2523 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-27-2524        TCGA-27-2526        TCGA-27-2528        TCGA-28-1747 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-28-1753        TCGA-28-2509        TCGA-28-2510        TCGA-28-2513 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-28-2514        TCGA-28-5204        TCGA-28-5207        TCGA-28-5208 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-28-5209        TCGA-28-5213        TCGA-28-5215        TCGA-28-5216 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5220        TCGA-32-1970        TCGA-32-1980 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-32-1982        TCGA-32-2615        TCGA-32-2616        TCGA-32-2632 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-32-2634        TCGA-32-2638        TCGA-32-4213        TCGA-32-5222 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-41-2571        TCGA-41-2572        TCGA-41-3915        TCGA-41-4097 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-41-5651        TCGA-76-4925        TCGA-76-4926        TCGA-76-4928 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-76-4929        TCGA-76-4931 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 

Clustering(8) Variable = 4q gain
D8V1, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           3               144
  CLUS_2           4                92
  CLUS_3           5               147
  CLUS_4           1               112
D8V2, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           4               113
  CLUS_2           5               166
  CLUS_3           4               216
D8V3, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           6               133
  CLUS_2           5               150
  CLUS_3           0                73
  CLUS_4           1               103
D8V4, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           8               173
  CLUS_2           1               154
  CLUS_3           3               132
D8V5, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           2               159
  CLUS_2           8               180
  CLUS_3           4               208
D8V6, multiclass
[1] "Remove cluster labels:" "4Q GAIN CNV"           
clus
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                2               107 
       TCGA-06-0650        TCGA-06-1804        TCGA-06-1806        TCGA-06-5408 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-06-6388 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-6389        TCGA-06-6390        TCGA-06-6391        TCGA-06-6693 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-6694        TCGA-06-6695        TCGA-06-6698        TCGA-06-6699 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-6700        TCGA-06-6701        TCGA-12-5295        TCGA-12-5299 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-12-5301        TCGA-14-0740        TCGA-14-0781        TCGA-14-0862 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-14-1043        TCGA-14-1395        TCGA-14-1450        TCGA-15-1444 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-19-4065        TCGA-19-5947        TCGA-19-5950        TCGA-19-5951 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-19-5952        TCGA-19-5953        TCGA-19-5954        TCGA-19-5955 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-19-5958        TCGA-19-5959        TCGA-19-5960        TCGA-26-1442 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-26-5132        TCGA-26-5133        TCGA-26-5134        TCGA-26-5135 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-26-5136        TCGA-26-5139        TCGA-26-6173        TCGA-26-6174 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-28-2501        TCGA-28-2510        TCGA-28-5204        TCGA-28-5207 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-28-5208        TCGA-28-5209        TCGA-28-5211        TCGA-28-5213 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-28-5214        TCGA-28-5215        TCGA-28-5216        TCGA-28-5218 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-28-5219        TCGA-28-5220        TCGA-28-6450        TCGA-32-1979 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-32-1980        TCGA-32-5222        TCGA-41-5651        TCGA-41-6646 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-74-6573        TCGA-74-6575        TCGA-74-6577        TCGA-74-6578 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-74-6581        TCGA-74-6584        TCGA-76-4925        TCGA-76-4926 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-4934 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-76-4935        TCGA-76-6191        TCGA-76-6192        TCGA-76-6193 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-76-6280        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-76-6286        TCGA-76-6656        TCGA-76-6657        TCGA-76-6660 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-76-6661        TCGA-76-6662        TCGA-76-6663        TCGA-76-6664 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-81-5910        TCGA-81-5911        TCGA-87-5896 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V7, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           3                51
  CLUS_2           1                57
  CLUS_3           0                44
  CLUS_4           1                44
D8V8, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           0                64
  CLUS_2           2                31
  CLUS_3           3               101
D8V9, multiclass
[1] "Remove cluster labels:" "4Q GAIN CNV"           
clus
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                1               146 
       TCGA-02-0047        TCGA-02-0055        TCGA-02-2483        TCGA-02-2485 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-02-2486        TCGA-06-0125        TCGA-06-0129        TCGA-06-0130 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0132        TCGA-06-0138        TCGA-06-0141        TCGA-06-0157 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0158        TCGA-06-0168        TCGA-06-0178        TCGA-06-0184 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0187        TCGA-06-0190        TCGA-06-0210        TCGA-06-0211 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0219        TCGA-06-0238        TCGA-06-0644        TCGA-06-0645 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0646        TCGA-06-0649        TCGA-06-0686        TCGA-06-0743 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0744        TCGA-06-0745        TCGA-06-0747        TCGA-06-0749 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0750        TCGA-06-0878        TCGA-06-0882        TCGA-06-1804 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-2557        TCGA-06-2558        TCGA-06-2559        TCGA-06-2561 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-2562        TCGA-06-2563        TCGA-06-2564        TCGA-06-2565 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-2567        TCGA-06-2569        TCGA-06-2570        TCGA-06-5408 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-08-0386 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-12-0616        TCGA-12-0618        TCGA-12-0619        TCGA-12-0821 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-12-3650        TCGA-12-3652        TCGA-12-3653        TCGA-12-5295 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-12-5299        TCGA-14-0781        TCGA-14-0787        TCGA-14-0789 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-14-0790        TCGA-14-0817        TCGA-14-1034        TCGA-14-1823 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-14-1825        TCGA-14-1829        TCGA-14-2554        TCGA-15-0742 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-15-1444        TCGA-16-0846        TCGA-16-1045        TCGA-19-1390 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-19-1787        TCGA-19-2619        TCGA-19-2620        TCGA-19-2624 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-19-2625        TCGA-19-2629        TCGA-19-4065        TCGA-19-5960 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-27-1830 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-27-1831        TCGA-27-1832        TCGA-27-1834        TCGA-27-1835 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-27-1837        TCGA-27-2519        TCGA-27-2521        TCGA-27-2523 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-27-2524        TCGA-27-2526        TCGA-27-2528        TCGA-28-1747 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-28-1753        TCGA-28-2509        TCGA-28-2510        TCGA-28-2513 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-28-2514        TCGA-28-5204        TCGA-28-5207        TCGA-28-5208 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-28-5209        TCGA-28-5213        TCGA-28-5215        TCGA-28-5216 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5220        TCGA-32-1970        TCGA-32-1980 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-32-1982        TCGA-32-2615        TCGA-32-2616        TCGA-32-2632 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-32-2634        TCGA-32-2638        TCGA-32-4213        TCGA-32-5222 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-41-2571        TCGA-41-2572        TCGA-41-3915        TCGA-41-4097 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-41-5651        TCGA-76-4925        TCGA-76-4926        TCGA-76-4928 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-76-4929        TCGA-76-4931 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V10, multiclass
[1] "Remove cluster labels:" "4Q GAIN CNV"           
clus
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                1               146 
       TCGA-02-0047        TCGA-02-0055        TCGA-02-2483        TCGA-02-2485 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-02-2486        TCGA-06-0125        TCGA-06-0129        TCGA-06-0130 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0132        TCGA-06-0138        TCGA-06-0141        TCGA-06-0157 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0158        TCGA-06-0168        TCGA-06-0178        TCGA-06-0184 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0187        TCGA-06-0190        TCGA-06-0210        TCGA-06-0211 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0219        TCGA-06-0238        TCGA-06-0644        TCGA-06-0645 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0646        TCGA-06-0649        TCGA-06-0686        TCGA-06-0743 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0744        TCGA-06-0745        TCGA-06-0747        TCGA-06-0749 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0750        TCGA-06-0878        TCGA-06-0882        TCGA-06-1804 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-2557        TCGA-06-2558        TCGA-06-2559        TCGA-06-2561 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-2562        TCGA-06-2563        TCGA-06-2564        TCGA-06-2565 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-2567        TCGA-06-2569        TCGA-06-2570        TCGA-06-5408 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-08-0386 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-12-0616        TCGA-12-0618        TCGA-12-0619        TCGA-12-0821 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-12-3650        TCGA-12-3652        TCGA-12-3653        TCGA-12-5295 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-12-5299        TCGA-14-0781        TCGA-14-0787        TCGA-14-0789 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-14-0790        TCGA-14-0817        TCGA-14-1034        TCGA-14-1823 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-14-1825        TCGA-14-1829        TCGA-14-2554        TCGA-15-0742 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-15-1444        TCGA-16-0846        TCGA-16-1045        TCGA-19-1390 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-19-1787        TCGA-19-2619        TCGA-19-2620        TCGA-19-2624 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-19-2625        TCGA-19-2629        TCGA-19-4065        TCGA-19-5960 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-27-1830 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-27-1831        TCGA-27-1832        TCGA-27-1834        TCGA-27-1835 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-27-1837        TCGA-27-2519        TCGA-27-2521        TCGA-27-2523 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-27-2524        TCGA-27-2526        TCGA-27-2528        TCGA-28-1747 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-28-1753        TCGA-28-2509        TCGA-28-2510        TCGA-28-2513 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-28-2514        TCGA-28-5204        TCGA-28-5207        TCGA-28-5208 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-28-5209        TCGA-28-5213        TCGA-28-5215        TCGA-28-5216 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5220        TCGA-32-1970        TCGA-32-1980 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-32-1982        TCGA-32-2615        TCGA-32-2616        TCGA-32-2632 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-32-2634        TCGA-32-2638        TCGA-32-4213        TCGA-32-5222 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-41-2571        TCGA-41-2572        TCGA-41-3915        TCGA-41-4097 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-41-5651        TCGA-76-4925        TCGA-76-4926        TCGA-76-4928 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-76-4929        TCGA-76-4931 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 

Clustering(9) Variable = 5p gain
D9V1, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          11               136
  CLUS_2           6                90
  CLUS_3           5               147
  CLUS_4           4               109
D9V2, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           6               111
  CLUS_2           4               167
  CLUS_3          16               204
D9V3, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          10               129
  CLUS_2           5               150
  CLUS_3           4                69
  CLUS_4           9                95
D9V4, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          10               171
  CLUS_2          12               143
  CLUS_3           6               129
D9V5, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          17               144
  CLUS_2           7               181
  CLUS_3           6               206
D9V6, multiclass
[1] "Remove cluster labels:" "5P GAIN CNV"           
clus
      5P GAIN CNV 5P GAIN WILD-TYPE 
                2               107 
       TCGA-06-0650        TCGA-06-1804        TCGA-06-5408        TCGA-06-5410 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-06-5411        TCGA-06-5412        TCGA-06-5413        TCGA-06-5414 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-06-5415        TCGA-06-5416        TCGA-06-5418        TCGA-06-5856 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-06-5858        TCGA-06-5859        TCGA-06-6388        TCGA-06-6389 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-06-6390        TCGA-06-6391        TCGA-06-6693        TCGA-06-6694 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-06-6695        TCGA-06-6697        TCGA-06-6698        TCGA-06-6699 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-06-6700        TCGA-06-6701        TCGA-12-5295        TCGA-12-5299 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-12-5301        TCGA-14-0740        TCGA-14-0781        TCGA-14-0862 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-14-1043        TCGA-14-1395        TCGA-14-1450        TCGA-15-1444 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-19-4065        TCGA-19-5947        TCGA-19-5950        TCGA-19-5951 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-19-5952        TCGA-19-5953        TCGA-19-5954        TCGA-19-5955 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-19-5956        TCGA-19-5958        TCGA-19-5959        TCGA-19-5960 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-26-6173 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-26-6174        TCGA-28-2501        TCGA-28-2510        TCGA-28-5204 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-28-5207        TCGA-28-5208        TCGA-28-5209        TCGA-28-5211 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-28-5213        TCGA-28-5214        TCGA-28-5215        TCGA-28-5218 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-28-5219        TCGA-28-5220        TCGA-28-6450        TCGA-32-1979 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-32-1980        TCGA-32-5222        TCGA-41-5651        TCGA-41-6646 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-74-6573        TCGA-74-6575        TCGA-74-6577        TCGA-74-6578 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-74-6581        TCGA-74-6584        TCGA-76-4925        TCGA-76-4926 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-4934 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-76-4935        TCGA-76-6191        TCGA-76-6192        TCGA-76-6193 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-76-6280        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-76-6286        TCGA-76-6656        TCGA-76-6657        TCGA-76-6660 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-76-6661        TCGA-76-6662        TCGA-76-6663        TCGA-76-6664 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-81-5910        TCGA-81-5911        TCGA-87-5896 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
D9V7, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           0                54
  CLUS_2           3                55
  CLUS_3           1                43
  CLUS_4           0                45
D9V8, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           2                62
  CLUS_2           0                33
  CLUS_3           2               102
D9V9, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           1                43
  CLUS_2           5                62
  CLUS_3           0                36
D9V10, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           5                61
  CLUS_2           0                21
  CLUS_3           1                59

Clustering(10) Variable = 5q gain
D10V1, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          10               137
  CLUS_2           2                94
  CLUS_3           5               147
  CLUS_4           3               110
D10V2, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           6               111
  CLUS_2           2               169
  CLUS_3          12               208
D10V3, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           8               131
  CLUS_2           2               153
  CLUS_3           3                70
  CLUS_4           8                96
D10V4, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           8               173
  CLUS_2          10               145
  CLUS_3           3               132
D10V5, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          13               148
  CLUS_2           4               184
  CLUS_3           6               206
D10V6, multiclass
[1] "Remove cluster labels:" "5Q GAIN CNV"           
clus
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
                2               107 
       TCGA-06-0650        TCGA-06-1804        TCGA-06-5408        TCGA-06-5410 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-5411        TCGA-06-5412        TCGA-06-5413        TCGA-06-5414 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-5415        TCGA-06-5416        TCGA-06-5418        TCGA-06-5856 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-5858        TCGA-06-5859        TCGA-06-6388        TCGA-06-6389 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-6390        TCGA-06-6391        TCGA-06-6693        TCGA-06-6694 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-6695        TCGA-06-6697        TCGA-06-6698        TCGA-06-6699 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-6700        TCGA-06-6701        TCGA-12-5295        TCGA-12-5299 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-12-5301        TCGA-14-0740        TCGA-14-0781        TCGA-14-0862 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-14-1043        TCGA-14-1395        TCGA-14-1450        TCGA-15-1444 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-4065        TCGA-19-5947        TCGA-19-5950        TCGA-19-5951 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-5952        TCGA-19-5953        TCGA-19-5954        TCGA-19-5955 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-5956        TCGA-19-5958        TCGA-19-5959        TCGA-19-5960 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-26-6173 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-26-6174        TCGA-28-2501        TCGA-28-2510        TCGA-28-5204 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-28-5207        TCGA-28-5208        TCGA-28-5209        TCGA-28-5211 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-28-5213        TCGA-28-5214        TCGA-28-5215        TCGA-28-5218 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-28-5219        TCGA-28-5220        TCGA-28-6450        TCGA-32-1979 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-32-1980        TCGA-32-5222        TCGA-41-5651        TCGA-41-6646 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-74-6573        TCGA-74-6575        TCGA-74-6577        TCGA-74-6578 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-74-6581        TCGA-74-6584        TCGA-76-4925        TCGA-76-4926 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-4934 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-4935        TCGA-76-6191        TCGA-76-6192        TCGA-76-6193 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-6280        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-6286        TCGA-76-6656        TCGA-76-6657        TCGA-76-6660 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-6661        TCGA-76-6662        TCGA-76-6663        TCGA-76-6664 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-81-5910        TCGA-81-5911        TCGA-87-5896 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
D10V7, multiclass
[1] "Remove cluster labels:" "5Q GAIN CNV"           
clus
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
                2               199 
       TCGA-02-0003        TCGA-02-0011        TCGA-02-0014        TCGA-02-0068 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-02-0069        TCGA-02-0116        TCGA-02-2470        TCGA-02-2485 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-0125        TCGA-06-0126        TCGA-06-0128        TCGA-06-0129 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-0130        TCGA-06-0154        TCGA-06-0155        TCGA-06-0171 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-0189        TCGA-06-0238        TCGA-06-0644        TCGA-06-0650 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-0875        TCGA-06-0876        TCGA-06-0877        TCGA-06-0878 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-0879        TCGA-06-0882        TCGA-06-0939        TCGA-06-1084 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-1086        TCGA-06-1087        TCGA-06-1800        TCGA-06-1802 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-1804        TCGA-06-1805        TCGA-06-2557        TCGA-06-2558 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-2559        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2566        TCGA-06-2567        TCGA-06-2570 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-5408        TCGA-06-5410        TCGA-06-5411        TCGA-06-5412 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-5413        TCGA-06-5414        TCGA-06-5415        TCGA-06-5416 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-5418        TCGA-06-5856        TCGA-06-5858        TCGA-06-5859 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-6388        TCGA-06-6389        TCGA-06-6390        TCGA-06-6391 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-6693        TCGA-06-6694        TCGA-06-6695        TCGA-06-6697 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-6698        TCGA-06-6699        TCGA-06-6700        TCGA-06-6701 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-08-0245        TCGA-08-0344        TCGA-08-0345        TCGA-08-0346 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-08-0347        TCGA-08-0348        TCGA-08-0349        TCGA-08-0350 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-08-0351        TCGA-08-0352        TCGA-08-0353        TCGA-08-0354 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-08-0355        TCGA-08-0356        TCGA-08-0357        TCGA-08-0358 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-08-0359        TCGA-08-0375        TCGA-08-0380        TCGA-08-0386 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-08-0389        TCGA-08-0390        TCGA-08-0392        TCGA-12-0691 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-12-0692        TCGA-12-1598        TCGA-12-1599        TCGA-12-3646 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-12-3649        TCGA-12-3650        TCGA-12-3651        TCGA-12-3652 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-12-3653        TCGA-12-5295        TCGA-12-5301        TCGA-14-0813 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-14-0862        TCGA-14-0871        TCGA-15-1446        TCGA-15-1447 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-15-1449        TCGA-16-0846        TCGA-16-1460        TCGA-19-0957 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-0962        TCGA-19-1386        TCGA-19-1389        TCGA-19-1390 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-1392        TCGA-19-1786        TCGA-19-1789        TCGA-19-1791 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-2619        TCGA-19-2620        TCGA-19-2625        TCGA-19-2631 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-5947        TCGA-19-5950        TCGA-19-5951        TCGA-19-5952 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-5953        TCGA-19-5954        TCGA-19-5955        TCGA-19-5956 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-5958        TCGA-19-5959        TCGA-19-5960        TCGA-26-1440 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-26-6173        TCGA-26-6174        TCGA-27-1830        TCGA-27-1831 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-27-1832        TCGA-27-1833        TCGA-27-1834        TCGA-27-1836 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-27-2518        TCGA-27-2528        TCGA-28-1746        TCGA-28-1747 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-28-1750        TCGA-28-1752        TCGA-28-1753        TCGA-28-1757 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-28-2501        TCGA-28-5208        TCGA-28-5214        TCGA-32-1970 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-32-1976        TCGA-32-1978        TCGA-32-1982        TCGA-32-1986 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-32-1987        TCGA-32-1991        TCGA-32-4210        TCGA-32-4211 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-32-5222        TCGA-41-2573        TCGA-41-2575        TCGA-41-3392 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-41-3393        TCGA-41-3915        TCGA-41-4097        TCGA-41-5651 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4926 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-6192 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-6193        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-6656        TCGA-76-6657        TCGA-76-6660        TCGA-76-6662 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-6663        TCGA-76-6664        TCGA-81-5910 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
D10V8, multiclass
[1] "Remove cluster labels:" "5Q GAIN CNV"           
clus
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
                2               199 
       TCGA-02-0003        TCGA-02-0011        TCGA-02-0014        TCGA-02-0068 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-02-0069        TCGA-02-0116        TCGA-02-2470        TCGA-02-2485 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-0125        TCGA-06-0126        TCGA-06-0128        TCGA-06-0129 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-0130        TCGA-06-0154        TCGA-06-0155        TCGA-06-0171 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-0189        TCGA-06-0238        TCGA-06-0644        TCGA-06-0650 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-0875        TCGA-06-0876        TCGA-06-0877        TCGA-06-0878 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-0879        TCGA-06-0882        TCGA-06-0939        TCGA-06-1084 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-1086        TCGA-06-1087        TCGA-06-1800        TCGA-06-1802 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-1804        TCGA-06-1805        TCGA-06-2557        TCGA-06-2558 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-2559        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2566        TCGA-06-2567        TCGA-06-2570 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-5408        TCGA-06-5410        TCGA-06-5411        TCGA-06-5412 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-5413        TCGA-06-5414        TCGA-06-5415        TCGA-06-5416 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-5418        TCGA-06-5856        TCGA-06-5858        TCGA-06-5859 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-6388        TCGA-06-6389        TCGA-06-6390        TCGA-06-6391 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-6693        TCGA-06-6694        TCGA-06-6695        TCGA-06-6697 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-6698        TCGA-06-6699        TCGA-06-6700        TCGA-06-6701 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-08-0245        TCGA-08-0344        TCGA-08-0345        TCGA-08-0346 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-08-0347        TCGA-08-0348        TCGA-08-0349        TCGA-08-0350 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-08-0351        TCGA-08-0352        TCGA-08-0353        TCGA-08-0354 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-08-0355        TCGA-08-0356        TCGA-08-0357        TCGA-08-0358 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-08-0359        TCGA-08-0375        TCGA-08-0380        TCGA-08-0386 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-08-0389        TCGA-08-0390        TCGA-08-0392        TCGA-12-0691 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-12-0692        TCGA-12-1598        TCGA-12-1599        TCGA-12-3646 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-12-3649        TCGA-12-3650        TCGA-12-3651        TCGA-12-3652 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-12-3653        TCGA-12-5295        TCGA-12-5301        TCGA-14-0813 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-14-0862        TCGA-14-0871        TCGA-15-1446        TCGA-15-1447 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-15-1449        TCGA-16-0846        TCGA-16-1460        TCGA-19-0957 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-0962        TCGA-19-1386        TCGA-19-1389        TCGA-19-1390 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-1392        TCGA-19-1786        TCGA-19-1789        TCGA-19-1791 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-2619        TCGA-19-2620        TCGA-19-2625        TCGA-19-2631 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-5947        TCGA-19-5950        TCGA-19-5951        TCGA-19-5952 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-5953        TCGA-19-5954        TCGA-19-5955        TCGA-19-5956 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-5958        TCGA-19-5959        TCGA-19-5960        TCGA-26-1440 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-26-6173        TCGA-26-6174        TCGA-27-1830        TCGA-27-1831 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-27-1832        TCGA-27-1833        TCGA-27-1834        TCGA-27-1836 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-27-2518        TCGA-27-2528        TCGA-28-1746        TCGA-28-1747 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-28-1750        TCGA-28-1752        TCGA-28-1753        TCGA-28-1757 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-28-2501        TCGA-28-5208        TCGA-28-5214        TCGA-32-1970 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-32-1976        TCGA-32-1978        TCGA-32-1982        TCGA-32-1986 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-32-1987        TCGA-32-1991        TCGA-32-4210        TCGA-32-4211 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-32-5222        TCGA-41-2573        TCGA-41-2575        TCGA-41-3392 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-41-3393        TCGA-41-3915        TCGA-41-4097        TCGA-41-5651 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4926 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-6192 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-6193        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-6656        TCGA-76-6657        TCGA-76-6660        TCGA-76-6662 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-6663        TCGA-76-6664        TCGA-81-5910 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
D10V9, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           1                43
  CLUS_2           4                63
  CLUS_3           0                36
D10V10, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           4                62
  CLUS_2           0                21
  CLUS_3           1                59

Clustering(11) Variable = 6p gain
D11V1, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           2               145
  CLUS_2           2                94
  CLUS_3           1               151
  CLUS_4           1               112
D11V2, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           1               116
  CLUS_2           3               168
  CLUS_3           2               218
D11V3, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           1               138
  CLUS_2           3               152
  CLUS_3           0                73
  CLUS_4           2               102
D11V4, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           1               180
  CLUS_2           2               153
  CLUS_3           3               132
D11V5, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           1               160
  CLUS_2           5               183
  CLUS_3           1               211
D11V6, multiclass
[1] "Remove cluster labels:" "6P GAIN CNV"           
clus
      6P GAIN CNV 6P GAIN WILD-TYPE 
                1               108 
       TCGA-06-0650        TCGA-06-1804        TCGA-06-1806        TCGA-06-5408 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-06-6388 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-6389        TCGA-06-6390        TCGA-06-6391        TCGA-06-6693 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-6694        TCGA-06-6695        TCGA-06-6697        TCGA-06-6698 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-6699        TCGA-06-6700        TCGA-06-6701        TCGA-12-5295 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-12-5299        TCGA-12-5301        TCGA-14-0740        TCGA-14-0781 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-14-0862        TCGA-14-1043        TCGA-14-1395        TCGA-14-1450 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-15-1444        TCGA-19-4065        TCGA-19-5947        TCGA-19-5950 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-5951        TCGA-19-5952        TCGA-19-5953        TCGA-19-5954 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-5955        TCGA-19-5956        TCGA-19-5958        TCGA-19-5959 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-5960        TCGA-26-1442        TCGA-26-5132        TCGA-26-5133 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-26-5134        TCGA-26-5135        TCGA-26-5136        TCGA-26-5139 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-26-6173        TCGA-26-6174        TCGA-28-2501        TCGA-28-2510 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-28-5204        TCGA-28-5207        TCGA-28-5208        TCGA-28-5209 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-28-5211        TCGA-28-5213        TCGA-28-5214        TCGA-28-5215 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-28-5216        TCGA-28-5218        TCGA-28-5219        TCGA-28-5220 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-28-6450        TCGA-32-1979        TCGA-32-1980        TCGA-32-5222 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-41-5651        TCGA-41-6646        TCGA-74-6573        TCGA-74-6575 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-74-6577        TCGA-74-6578        TCGA-74-6581        TCGA-74-6584 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-4925        TCGA-76-4926        TCGA-76-4928        TCGA-76-4929 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-4931        TCGA-76-4934        TCGA-76-4935        TCGA-76-6191 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-6192        TCGA-76-6193        TCGA-76-6280        TCGA-76-6282 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-6283        TCGA-76-6285        TCGA-76-6286        TCGA-76-6656 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-6657        TCGA-76-6660        TCGA-76-6661        TCGA-76-6662 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-6663        TCGA-76-6664        TCGA-81-5910        TCGA-87-5896 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
D11V7, multiclass
[1] "Remove cluster labels:" "6P GAIN CNV"           
clus
      6P GAIN CNV 6P GAIN WILD-TYPE 
                2               199 
       TCGA-02-0003        TCGA-02-0011        TCGA-02-0014        TCGA-02-0068 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-02-0116        TCGA-02-2470        TCGA-02-2485        TCGA-06-0125 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-0126        TCGA-06-0128        TCGA-06-0129        TCGA-06-0130 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-0154        TCGA-06-0155        TCGA-06-0171        TCGA-06-0189 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-0238        TCGA-06-0644        TCGA-06-0650        TCGA-06-0875 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-0876        TCGA-06-0877        TCGA-06-0878        TCGA-06-0879 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-0882        TCGA-06-0939        TCGA-06-1084        TCGA-06-1086 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-1087        TCGA-06-1800        TCGA-06-1802        TCGA-06-1804 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-1805        TCGA-06-1806        TCGA-06-2557        TCGA-06-2558 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-2559        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2566        TCGA-06-2567        TCGA-06-2570 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-5408        TCGA-06-5410        TCGA-06-5411        TCGA-06-5412 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-5413        TCGA-06-5414        TCGA-06-5415        TCGA-06-5416 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-5418        TCGA-06-5856        TCGA-06-5858        TCGA-06-5859 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-6388        TCGA-06-6389        TCGA-06-6390        TCGA-06-6391 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-6693        TCGA-06-6694        TCGA-06-6695        TCGA-06-6697 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-6698        TCGA-06-6699        TCGA-06-6700        TCGA-06-6701 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-08-0245        TCGA-08-0344        TCGA-08-0345        TCGA-08-0346 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-08-0347        TCGA-08-0348        TCGA-08-0349        TCGA-08-0350 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-08-0351        TCGA-08-0352        TCGA-08-0353        TCGA-08-0354 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-08-0355        TCGA-08-0356        TCGA-08-0357        TCGA-08-0358 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-08-0359        TCGA-08-0375        TCGA-08-0380        TCGA-08-0386 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-08-0389        TCGA-08-0390        TCGA-08-0392        TCGA-12-0691 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-12-0692        TCGA-12-1598        TCGA-12-1599        TCGA-12-3646 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-12-3649        TCGA-12-3650        TCGA-12-3651        TCGA-12-3652 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-12-3653        TCGA-12-5295        TCGA-12-5301        TCGA-14-0813 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-14-0862        TCGA-14-0871        TCGA-14-1823        TCGA-15-1446 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-15-1449        TCGA-16-0846        TCGA-16-1460        TCGA-19-0957 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-0962        TCGA-19-1386        TCGA-19-1389        TCGA-19-1390 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-1392        TCGA-19-1786        TCGA-19-1789        TCGA-19-1791 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-2619        TCGA-19-2620        TCGA-19-2625        TCGA-19-2631 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-5947        TCGA-19-5950        TCGA-19-5951        TCGA-19-5952 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-5953        TCGA-19-5954        TCGA-19-5955        TCGA-19-5956 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-5958        TCGA-19-5959        TCGA-19-5960        TCGA-26-1440 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-26-6173        TCGA-26-6174        TCGA-27-1830        TCGA-27-1831 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-27-1832        TCGA-27-1833        TCGA-27-1834        TCGA-27-1836 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-27-2518        TCGA-27-2528        TCGA-28-1746        TCGA-28-1747 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-28-1750        TCGA-28-1752        TCGA-28-1753        TCGA-28-1757 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-28-2501        TCGA-28-5208        TCGA-28-5214        TCGA-32-1970 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-32-1976        TCGA-32-1978        TCGA-32-1982        TCGA-32-1986 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-32-1987        TCGA-32-1991        TCGA-32-4210        TCGA-32-4211 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-32-5222        TCGA-41-2573        TCGA-41-2575        TCGA-41-3392 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-41-3393        TCGA-41-3915        TCGA-41-4097        TCGA-41-5651 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4926 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-6192 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-6193        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-6656        TCGA-76-6657        TCGA-76-6660        TCGA-76-6662 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-6663        TCGA-76-6664        TCGA-81-5910 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
D11V8, multiclass
[1] "Remove cluster labels:" "6P GAIN CNV"           
clus
      6P GAIN CNV 6P GAIN WILD-TYPE 
                2               199 
       TCGA-02-0003        TCGA-02-0011        TCGA-02-0014        TCGA-02-0068 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-02-0116        TCGA-02-2470        TCGA-02-2485        TCGA-06-0125 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-0126        TCGA-06-0128        TCGA-06-0129        TCGA-06-0130 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-0154        TCGA-06-0155        TCGA-06-0171        TCGA-06-0189 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-0238        TCGA-06-0644        TCGA-06-0650        TCGA-06-0875 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-0876        TCGA-06-0877        TCGA-06-0878        TCGA-06-0879 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-0882        TCGA-06-0939        TCGA-06-1084        TCGA-06-1086 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-1087        TCGA-06-1800        TCGA-06-1802        TCGA-06-1804 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-1805        TCGA-06-1806        TCGA-06-2557        TCGA-06-2558 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-2559        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2566        TCGA-06-2567        TCGA-06-2570 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-5408        TCGA-06-5410        TCGA-06-5411        TCGA-06-5412 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-5413        TCGA-06-5414        TCGA-06-5415        TCGA-06-5416 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-5418        TCGA-06-5856        TCGA-06-5858        TCGA-06-5859 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-6388        TCGA-06-6389        TCGA-06-6390        TCGA-06-6391 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-6693        TCGA-06-6694        TCGA-06-6695        TCGA-06-6697 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-6698        TCGA-06-6699        TCGA-06-6700        TCGA-06-6701 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-08-0245        TCGA-08-0344        TCGA-08-0345        TCGA-08-0346 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-08-0347        TCGA-08-0348        TCGA-08-0349        TCGA-08-0350 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-08-0351        TCGA-08-0352        TCGA-08-0353        TCGA-08-0354 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-08-0355        TCGA-08-0356        TCGA-08-0357        TCGA-08-0358 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-08-0359        TCGA-08-0375        TCGA-08-0380        TCGA-08-0386 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-08-0389        TCGA-08-0390        TCGA-08-0392        TCGA-12-0691 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-12-0692        TCGA-12-1598        TCGA-12-1599        TCGA-12-3646 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-12-3649        TCGA-12-3650        TCGA-12-3651        TCGA-12-3652 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-12-3653        TCGA-12-5295        TCGA-12-5301        TCGA-14-0813 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-14-0862        TCGA-14-0871        TCGA-14-1823        TCGA-15-1446 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-15-1449        TCGA-16-0846        TCGA-16-1460        TCGA-19-0957 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-0962        TCGA-19-1386        TCGA-19-1389        TCGA-19-1390 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-1392        TCGA-19-1786        TCGA-19-1789        TCGA-19-1791 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-2619        TCGA-19-2620        TCGA-19-2625        TCGA-19-2631 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-5947        TCGA-19-5950        TCGA-19-5951        TCGA-19-5952 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-5953        TCGA-19-5954        TCGA-19-5955        TCGA-19-5956 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-5958        TCGA-19-5959        TCGA-19-5960        TCGA-26-1440 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-26-6173        TCGA-26-6174        TCGA-27-1830        TCGA-27-1831 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-27-1832        TCGA-27-1833        TCGA-27-1834        TCGA-27-1836 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-27-2518        TCGA-27-2528        TCGA-28-1746        TCGA-28-1747 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-28-1750        TCGA-28-1752        TCGA-28-1753        TCGA-28-1757 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-28-2501        TCGA-28-5208        TCGA-28-5214        TCGA-32-1970 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-32-1976        TCGA-32-1978        TCGA-32-1982        TCGA-32-1986 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-32-1987        TCGA-32-1991        TCGA-32-4210        TCGA-32-4211 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-32-5222        TCGA-41-2573        TCGA-41-2575        TCGA-41-3392 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-41-3393        TCGA-41-3915        TCGA-41-4097        TCGA-41-5651 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4926 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-6192 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-6193        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-6656        TCGA-76-6657        TCGA-76-6660        TCGA-76-6662 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-6663        TCGA-76-6664        TCGA-81-5910 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
D11V9, multiclass
D11V10, multiclass

Clustering(12) Variable = 6q gain
D12V1, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           2               145
  CLUS_2           3                93
  CLUS_3           1               151
  CLUS_4           2               111
D12V2, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           1               116
  CLUS_2           4               167
  CLUS_3           3               217
D12V3, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           2               137
  CLUS_2           3               152
  CLUS_3           0                73
  CLUS_4           3               101
D12V4, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           1               180
  CLUS_2           3               152
  CLUS_3           4               131
D12V5, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           1               160
  CLUS_2           7               181
  CLUS_3           1               211
D12V6, multiclass
[1] "Remove cluster labels:" "6Q GAIN CNV"           
clus
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                1               108 
       TCGA-06-0650        TCGA-06-1804        TCGA-06-1806        TCGA-06-5408 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-06-6388 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-6389        TCGA-06-6390        TCGA-06-6391        TCGA-06-6693 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-6694        TCGA-06-6695        TCGA-06-6697        TCGA-06-6698 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-6699        TCGA-06-6700        TCGA-06-6701        TCGA-12-5295 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-5299        TCGA-12-5301        TCGA-14-0740        TCGA-14-0781 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-14-0862        TCGA-14-1043        TCGA-14-1395        TCGA-14-1450 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-15-1444        TCGA-19-4065        TCGA-19-5947        TCGA-19-5950 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-5951        TCGA-19-5952        TCGA-19-5953        TCGA-19-5954 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-5955        TCGA-19-5956        TCGA-19-5958        TCGA-19-5959 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-5960        TCGA-26-1442        TCGA-26-5132        TCGA-26-5133 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-26-5134        TCGA-26-5135        TCGA-26-5136        TCGA-26-5139 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-26-6173        TCGA-26-6174        TCGA-28-2501        TCGA-28-2510 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-5204        TCGA-28-5207        TCGA-28-5208        TCGA-28-5209 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-5211        TCGA-28-5213        TCGA-28-5214        TCGA-28-5215 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-5216        TCGA-28-5218        TCGA-28-5219        TCGA-28-5220 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-6450        TCGA-32-1979        TCGA-32-1980        TCGA-32-5222 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-41-5651        TCGA-41-6646        TCGA-74-6573        TCGA-74-6575 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-74-6577        TCGA-74-6578        TCGA-74-6581        TCGA-74-6584 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-4925        TCGA-76-4926        TCGA-76-4928        TCGA-76-4929 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-4931        TCGA-76-4934        TCGA-76-4935        TCGA-76-6191 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-6192        TCGA-76-6193        TCGA-76-6280        TCGA-76-6282 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-6283        TCGA-76-6285        TCGA-76-6286        TCGA-76-6656 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-6657        TCGA-76-6660        TCGA-76-6661        TCGA-76-6662 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-6663        TCGA-76-6664        TCGA-81-5910        TCGA-87-5896 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D12V7, multiclass
[1] "Remove cluster labels:" "6Q GAIN CNV"           
clus
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                2               199 
       TCGA-02-0003        TCGA-02-0011        TCGA-02-0014        TCGA-02-0068 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-02-0116        TCGA-02-2470        TCGA-02-2485        TCGA-06-0125 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0126        TCGA-06-0128        TCGA-06-0129        TCGA-06-0130 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0154        TCGA-06-0155        TCGA-06-0171        TCGA-06-0189 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0238        TCGA-06-0644        TCGA-06-0650        TCGA-06-0875 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0876        TCGA-06-0877        TCGA-06-0878        TCGA-06-0879 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0882        TCGA-06-0939        TCGA-06-1084        TCGA-06-1086 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-1087        TCGA-06-1800        TCGA-06-1802        TCGA-06-1804 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-1805        TCGA-06-1806        TCGA-06-2557        TCGA-06-2558 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-2559        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2566        TCGA-06-2567        TCGA-06-2570 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5408        TCGA-06-5410        TCGA-06-5411        TCGA-06-5412 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5413        TCGA-06-5414        TCGA-06-5415        TCGA-06-5416 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5418        TCGA-06-5856        TCGA-06-5858        TCGA-06-5859 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-6388        TCGA-06-6389        TCGA-06-6390        TCGA-06-6391 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-6693        TCGA-06-6694        TCGA-06-6695        TCGA-06-6697 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-6698        TCGA-06-6699        TCGA-06-6700        TCGA-06-6701 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-08-0245        TCGA-08-0344        TCGA-08-0345        TCGA-08-0346 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-08-0347        TCGA-08-0348        TCGA-08-0349        TCGA-08-0350 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-08-0351        TCGA-08-0352        TCGA-08-0353        TCGA-08-0354 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-08-0355        TCGA-08-0356        TCGA-08-0357        TCGA-08-0358 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-08-0359        TCGA-08-0375        TCGA-08-0380        TCGA-08-0386 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-08-0389        TCGA-08-0390        TCGA-08-0392        TCGA-12-0691 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-0692        TCGA-12-1598        TCGA-12-1599        TCGA-12-3646 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-3649        TCGA-12-3650        TCGA-12-3651        TCGA-12-3652 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-3653        TCGA-12-5295        TCGA-12-5301        TCGA-14-0813 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-14-0862        TCGA-14-0871        TCGA-14-1823        TCGA-15-1446 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-15-1449        TCGA-16-0846        TCGA-16-1460        TCGA-19-0957 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-0962        TCGA-19-1386        TCGA-19-1389        TCGA-19-1390 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-1392        TCGA-19-1786        TCGA-19-1789        TCGA-19-1791 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-2619        TCGA-19-2620        TCGA-19-2625        TCGA-19-2631 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-5947        TCGA-19-5950        TCGA-19-5951        TCGA-19-5952 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-5953        TCGA-19-5954        TCGA-19-5955        TCGA-19-5956 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-5958        TCGA-19-5959        TCGA-19-5960        TCGA-26-1440 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-26-6173        TCGA-26-6174        TCGA-27-1830        TCGA-27-1831 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-27-1832        TCGA-27-1833        TCGA-27-1834        TCGA-27-1836 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-27-2518        TCGA-27-2528        TCGA-28-1746        TCGA-28-1747 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-1750        TCGA-28-1752        TCGA-28-1753        TCGA-28-1757 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-2501        TCGA-28-5208        TCGA-28-5214        TCGA-32-1970 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-32-1976        TCGA-32-1978        TCGA-32-1982        TCGA-32-1986 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-32-1987        TCGA-32-1991        TCGA-32-4210        TCGA-32-4211 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-32-5222        TCGA-41-2573        TCGA-41-2575        TCGA-41-3392 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-41-3393        TCGA-41-3915        TCGA-41-4097        TCGA-41-5651 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4926 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-6192 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-6193        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-6656        TCGA-76-6657        TCGA-76-6660        TCGA-76-6662 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-6663        TCGA-76-6664        TCGA-81-5910 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D12V8, multiclass
[1] "Remove cluster labels:" "6Q GAIN CNV"           
clus
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                2               199 
       TCGA-02-0003        TCGA-02-0011        TCGA-02-0014        TCGA-02-0068 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-02-0116        TCGA-02-2470        TCGA-02-2485        TCGA-06-0125 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0126        TCGA-06-0128        TCGA-06-0129        TCGA-06-0130 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0154        TCGA-06-0155        TCGA-06-0171        TCGA-06-0189 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0238        TCGA-06-0644        TCGA-06-0650        TCGA-06-0875 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0876        TCGA-06-0877        TCGA-06-0878        TCGA-06-0879 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0882        TCGA-06-0939        TCGA-06-1084        TCGA-06-1086 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-1087        TCGA-06-1800        TCGA-06-1802        TCGA-06-1804 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-1805        TCGA-06-1806        TCGA-06-2557        TCGA-06-2558 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-2559        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2566        TCGA-06-2567        TCGA-06-2570 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5408        TCGA-06-5410        TCGA-06-5411        TCGA-06-5412 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5413        TCGA-06-5414        TCGA-06-5415        TCGA-06-5416 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5418        TCGA-06-5856        TCGA-06-5858        TCGA-06-5859 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-6388        TCGA-06-6389        TCGA-06-6390        TCGA-06-6391 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-6693        TCGA-06-6694        TCGA-06-6695        TCGA-06-6697 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-6698        TCGA-06-6699        TCGA-06-6700        TCGA-06-6701 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-08-0245        TCGA-08-0344        TCGA-08-0345        TCGA-08-0346 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-08-0347        TCGA-08-0348        TCGA-08-0349        TCGA-08-0350 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-08-0351        TCGA-08-0352        TCGA-08-0353        TCGA-08-0354 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-08-0355        TCGA-08-0356        TCGA-08-0357        TCGA-08-0358 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-08-0359        TCGA-08-0375        TCGA-08-0380        TCGA-08-0386 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-08-0389        TCGA-08-0390        TCGA-08-0392        TCGA-12-0691 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-0692        TCGA-12-1598        TCGA-12-1599        TCGA-12-3646 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-3649        TCGA-12-3650        TCGA-12-3651        TCGA-12-3652 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-3653        TCGA-12-5295        TCGA-12-5301        TCGA-14-0813 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-14-0862        TCGA-14-0871        TCGA-14-1823        TCGA-15-1446 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-15-1449        TCGA-16-0846        TCGA-16-1460        TCGA-19-0957 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-0962        TCGA-19-1386        TCGA-19-1389        TCGA-19-1390 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-1392        TCGA-19-1786        TCGA-19-1789        TCGA-19-1791 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-2619        TCGA-19-2620        TCGA-19-2625        TCGA-19-2631 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-5947        TCGA-19-5950        TCGA-19-5951        TCGA-19-5952 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-5953        TCGA-19-5954        TCGA-19-5955        TCGA-19-5956 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-5958        TCGA-19-5959        TCGA-19-5960        TCGA-26-1440 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-26-6173        TCGA-26-6174        TCGA-27-1830        TCGA-27-1831 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-27-1832        TCGA-27-1833        TCGA-27-1834        TCGA-27-1836 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-27-2518        TCGA-27-2528        TCGA-28-1746        TCGA-28-1747 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-1750        TCGA-28-1752        TCGA-28-1753        TCGA-28-1757 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-2501        TCGA-28-5208        TCGA-28-5214        TCGA-32-1970 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-32-1976        TCGA-32-1978        TCGA-32-1982        TCGA-32-1986 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-32-1987        TCGA-32-1991        TCGA-32-4210        TCGA-32-4211 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-32-5222        TCGA-41-2573        TCGA-41-2575        TCGA-41-3392 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-41-3393        TCGA-41-3915        TCGA-41-4097        TCGA-41-5651 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4926 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-6192 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-6193        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-6656        TCGA-76-6657        TCGA-76-6660        TCGA-76-6662 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-6663        TCGA-76-6664        TCGA-81-5910 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D12V9, multiclass
[1] "Remove cluster labels:" "6Q GAIN CNV"           
clus
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                1               146 
       TCGA-02-0047        TCGA-02-0055        TCGA-02-2483        TCGA-02-2485 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-02-2486        TCGA-06-0125        TCGA-06-0129        TCGA-06-0130 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0132        TCGA-06-0138        TCGA-06-0141        TCGA-06-0157 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0158        TCGA-06-0168        TCGA-06-0174        TCGA-06-0178 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0184        TCGA-06-0187        TCGA-06-0190        TCGA-06-0210 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0211        TCGA-06-0219        TCGA-06-0238        TCGA-06-0644 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0645        TCGA-06-0646        TCGA-06-0649        TCGA-06-0686 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0743        TCGA-06-0744        TCGA-06-0745        TCGA-06-0747 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0749        TCGA-06-0750        TCGA-06-0878        TCGA-06-0882 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-1804        TCGA-06-2557        TCGA-06-2558        TCGA-06-2559 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-2561        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2567        TCGA-06-2570        TCGA-06-5408 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-08-0386 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-0616        TCGA-12-0618        TCGA-12-0619        TCGA-12-0821 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-3650        TCGA-12-3652        TCGA-12-3653        TCGA-12-5295 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-5299        TCGA-14-0781        TCGA-14-0787        TCGA-14-0789 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-14-0790        TCGA-14-0817        TCGA-14-1034        TCGA-14-1823 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-14-1825        TCGA-14-1829        TCGA-14-2554        TCGA-15-0742 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-15-1444        TCGA-16-0846        TCGA-16-1045        TCGA-19-1390 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-1787        TCGA-19-2619        TCGA-19-2620        TCGA-19-2624 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-2625        TCGA-19-2629        TCGA-19-4065        TCGA-19-5960 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-27-1830 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-27-1831        TCGA-27-1832        TCGA-27-1834        TCGA-27-1835 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-27-1837        TCGA-27-2519        TCGA-27-2521        TCGA-27-2523 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-27-2524        TCGA-27-2526        TCGA-27-2528        TCGA-28-1747 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-1753        TCGA-28-2509        TCGA-28-2510        TCGA-28-2513 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-2514        TCGA-28-5204        TCGA-28-5207        TCGA-28-5208 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-5209        TCGA-28-5213        TCGA-28-5215        TCGA-28-5216 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5220        TCGA-32-1970        TCGA-32-1980 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-32-1982        TCGA-32-2615        TCGA-32-2616        TCGA-32-2632 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-32-2634        TCGA-32-2638        TCGA-32-4213        TCGA-32-5222 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-41-2571        TCGA-41-2572        TCGA-41-3915        TCGA-41-4097 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-41-5651        TCGA-76-4925        TCGA-76-4926        TCGA-76-4928 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-4929        TCGA-76-4931 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D12V10, multiclass
[1] "Remove cluster labels:" "6Q GAIN CNV"           
clus
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                1               146 
       TCGA-02-0047        TCGA-02-0055        TCGA-02-2483        TCGA-02-2485 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-02-2486        TCGA-06-0125        TCGA-06-0129        TCGA-06-0130 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0132        TCGA-06-0138        TCGA-06-0141        TCGA-06-0157 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0158        TCGA-06-0168        TCGA-06-0174        TCGA-06-0178 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0184        TCGA-06-0187        TCGA-06-0190        TCGA-06-0210 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0211        TCGA-06-0219        TCGA-06-0238        TCGA-06-0644 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0645        TCGA-06-0646        TCGA-06-0649        TCGA-06-0686 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0743        TCGA-06-0744        TCGA-06-0745        TCGA-06-0747 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0749        TCGA-06-0750        TCGA-06-0878        TCGA-06-0882 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-1804        TCGA-06-2557        TCGA-06-2558        TCGA-06-2559 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-2561        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2567        TCGA-06-2570        TCGA-06-5408 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-08-0386 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-0616        TCGA-12-0618        TCGA-12-0619        TCGA-12-0821 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-3650        TCGA-12-3652        TCGA-12-3653        TCGA-12-5295 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-5299        TCGA-14-0781        TCGA-14-0787        TCGA-14-0789 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-14-0790        TCGA-14-0817        TCGA-14-1034        TCGA-14-1823 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-14-1825        TCGA-14-1829        TCGA-14-2554        TCGA-15-0742 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-15-1444        TCGA-16-0846        TCGA-16-1045        TCGA-19-1390 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-1787        TCGA-19-2619        TCGA-19-2620        TCGA-19-2624 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-2625        TCGA-19-2629        TCGA-19-4065        TCGA-19-5960 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-27-1830 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-27-1831        TCGA-27-1832        TCGA-27-1834        TCGA-27-1835 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-27-1837        TCGA-27-2519        TCGA-27-2521        TCGA-27-2523 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-27-2524        TCGA-27-2526        TCGA-27-2528        TCGA-28-1747 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-1753        TCGA-28-2509        TCGA-28-2510        TCGA-28-2513 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-2514        TCGA-28-5204        TCGA-28-5207        TCGA-28-5208 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-5209        TCGA-28-5213        TCGA-28-5215        TCGA-28-5216 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5220        TCGA-32-1970        TCGA-32-1980 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-32-1982        TCGA-32-2615        TCGA-32-2616        TCGA-32-2632 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-32-2634        TCGA-32-2638        TCGA-32-4213        TCGA-32-5222 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-41-2571        TCGA-41-2572        TCGA-41-3915        TCGA-41-4097 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-41-5651        TCGA-76-4925        TCGA-76-4926        TCGA-76-4928 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-4929        TCGA-76-4931 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 

Clustering(13) Variable = 7p gain
D13V1, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1         123                24
  CLUS_2          63                33
  CLUS_3         129                23
  CLUS_4          74                39
D13V2, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          99                18
  CLUS_2         108                63
  CLUS_3         182                38
D13V3, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1         120                19
  CLUS_2         110                45
  CLUS_3          49                24
  CLUS_4          87                17
D13V4, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1         161                20
  CLUS_2         128                27
  CLUS_3          77                58
D13V5, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1         140                21
  CLUS_2         103                85
  CLUS_3         188                24
D13V6, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          29                10
  CLUS_2          24                 3
  CLUS_3          16                 0
  CLUS_4          15                12
D13V7, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          40                14
  CLUS_2          39                19
  CLUS_3          37                 7
  CLUS_4          43                 2
D13V8, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          54                10
  CLUS_2          25                 8
  CLUS_3          80                24
D13V9, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          28                16
  CLUS_2          56                11
  CLUS_3          25                11
D13V10, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          56                10
  CLUS_2          17                 4
  CLUS_3          36                24

Clustering(14) Variable = 7q gain
D14V1, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1         124                23
  CLUS_2          59                37
  CLUS_3         130                22
  CLUS_4          79                34
D14V2, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          99                18
  CLUS_2         113                58
  CLUS_3         180                40
D14V3, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1         121                18
  CLUS_2         109                46
  CLUS_3          51                22
  CLUS_4          86                18
D14V4, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1         156                25
  CLUS_2         128                27
  CLUS_3          83                52
D14V5, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1         137                24
  CLUS_2         108                80
  CLUS_3         191                21
D14V6, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          31                 8
  CLUS_2          24                 3
  CLUS_3          16                 0
  CLUS_4          15                12
D14V7, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          39                15
  CLUS_2          42                16
  CLUS_3          39                 5
  CLUS_4          41                 4
D14V8, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          55                 9
  CLUS_2          26                 7
  CLUS_3          80                24
D14V9, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          28                16
  CLUS_2          55                12
  CLUS_3          28                 8
D14V10, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          57                 9
  CLUS_2          16                 5
  CLUS_3          38                22

Clustering(15) Variable = 8p gain
D15V1, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           2               145
  CLUS_2          10                86
  CLUS_3           2               150
  CLUS_4          10               103
D15V2, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           2               115
  CLUS_2          11               160
  CLUS_3          11               209
D15V3, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           4               135
  CLUS_2           8               147
  CLUS_3           6                67
  CLUS_4           4               100
D15V4, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           3               178
  CLUS_2           7               148
  CLUS_3          12               123
D15V5, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          15               146
  CLUS_2           8               180
  CLUS_3           3               209
D15V6, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           1                38
  CLUS_2           0                27
  CLUS_3           0                16
  CLUS_4           3                24
D15V7, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           1                53
  CLUS_2           7                51
  CLUS_3           1                43
  CLUS_4           1                44
D15V8, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           1                63
  CLUS_2           0                33
  CLUS_3           9                95
D15V9, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           3                41
  CLUS_2           4                63
  CLUS_3           1                35
D15V10, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           5                61
  CLUS_2           0                21
  CLUS_3           3                57

Clustering(16) Variable = 8q gain
D16V1, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           3               144
  CLUS_2          11                85
  CLUS_3           3               149
  CLUS_4          11               102
D16V2, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           3               114
  CLUS_2          14               157
  CLUS_3          11               209
D16V3, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           5               134
  CLUS_2          13               142
  CLUS_3           5                68
  CLUS_4           4               100
D16V4, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           5               176
  CLUS_2           7               148
  CLUS_3          15               120
D16V5, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          15               146
  CLUS_2          12               176
  CLUS_3           4               208
D16V6, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           1                38
  CLUS_2           0                27
  CLUS_3           0                16
  CLUS_4           4                23
D16V7, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           1                53
  CLUS_2           7                51
  CLUS_3           1                43
  CLUS_4           1                44
D16V8, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           1                63
  CLUS_2           0                33
  CLUS_3           9                95
D16V9, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           5                39
  CLUS_2           4                63
  CLUS_3           1                35
D16V10, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           5                61
  CLUS_2           0                21
  CLUS_3           5                55

Clustering(17) Variable = 9p gain
D17V1, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           4               143
  CLUS_2           7                89
  CLUS_3           1               151
  CLUS_4           3               110
D17V2, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           0               117
  CLUS_2           7               164
  CLUS_3           8               212
D17V3, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           3               136
  CLUS_2           7               148
  CLUS_3           2                71
  CLUS_4           4               100
D17V4, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           6               175
  CLUS_2           2               153
  CLUS_3           8               127
D17V5, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           8               153
  CLUS_2           7               181
  CLUS_3           2               210
D17V6, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           2                37
  CLUS_2           0                27
  CLUS_3           0                16
  CLUS_4           2                25
D17V7, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           3                51
  CLUS_2           2                56
  CLUS_3           0                44
  CLUS_4           0                45
D17V8, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           0                64
  CLUS_2           1                32
  CLUS_3           4               100
D17V9, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           3                41
  CLUS_2           4                63
  CLUS_3           0                36
D17V10, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           4                62
  CLUS_2           0                21
  CLUS_3           3                57

Clustering(18) Variable = 9q gain
D18V1, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           8               139
  CLUS_2          10                86
  CLUS_3           6               146
  CLUS_4           6               107
D18V2, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           3               114
  CLUS_2          12               159
  CLUS_3          15               205
D18V3, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           6               133
  CLUS_2          14               141
  CLUS_3           4                69
  CLUS_4           7                97
D18V4, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1          12               169
  CLUS_2           7               148
  CLUS_3          12               123
D18V5, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1          12               149
  CLUS_2          13               175
  CLUS_3           8               204
D18V6, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           2                37
  CLUS_2           1                26
  CLUS_3           1                15
  CLUS_4           1                26
D18V7, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           3                51
  CLUS_2           3                55
  CLUS_3           0                44
  CLUS_4           1                44
D18V8, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           0                64
  CLUS_2           2                31
  CLUS_3           5                99
D18V9, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           4                40
  CLUS_2           5                62
  CLUS_3           1                35
D18V10, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           5                61
  CLUS_2           2                19
  CLUS_3           3                57

Clustering(19) Variable = 10p gain
D19V1, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            0                147
  CLUS_2            6                 90
  CLUS_3            0                152
  CLUS_4            5                108
D19V2, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            0                117
  CLUS_2            9                162
  CLUS_3            2                218
D19V3, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            0                139
  CLUS_2            7                148
  CLUS_3            3                 70
  CLUS_4            1                103
D19V4, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            1                180
  CLUS_2            1                154
  CLUS_3            9                126
D19V5, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            2                159
  CLUS_2            9                179
  CLUS_3            0                212
D19V6, multiclass
D19V7, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            1                 53
  CLUS_2            3                 55
  CLUS_3            0                 44
  CLUS_4            0                 45
D19V8, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            0                 64
  CLUS_2            1                 32
  CLUS_3            3                101
D19V9, multiclass
[1] "Remove cluster labels:" "10P GAIN CNV"          
clus
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 1                146 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2570         TCGA-06-5408 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-5410         TCGA-06-5411         TCGA-06-5412 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-5413         TCGA-06-5414         TCGA-06-5415 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-5416         TCGA-06-5418         TCGA-06-5856 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-5858         TCGA-06-5859         TCGA-08-0386 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-12-0616         TCGA-12-0618         TCGA-12-0619 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-12-0821         TCGA-12-3650         TCGA-12-3652 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-12-3653         TCGA-12-5295         TCGA-12-5299 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-14-0781         TCGA-14-0787         TCGA-14-0789 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-14-0790         TCGA-14-0817         TCGA-14-1034 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-14-1823         TCGA-14-1825         TCGA-14-1829 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-14-2554         TCGA-15-0742         TCGA-15-1444 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-16-0846         TCGA-16-1045         TCGA-19-1390 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2620 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-19-2624         TCGA-19-2625         TCGA-19-2629 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-19-4065         TCGA-19-5960         TCGA-26-1442 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-26-5135         TCGA-26-5136         TCGA-26-5139 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-27-1830         TCGA-27-1831         TCGA-27-1832 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1835         TCGA-27-1837 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-27-2519         TCGA-27-2521         TCGA-27-2523 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-27-2524         TCGA-27-2526         TCGA-27-2528 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-28-1747         TCGA-28-1753         TCGA-28-2509 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-28-2510         TCGA-28-2513         TCGA-28-2514 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5213         TCGA-28-5215 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-28-5216         TCGA-28-5218         TCGA-28-5220 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-32-1970         TCGA-32-1980         TCGA-32-1982 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-32-2615         TCGA-32-2616         TCGA-32-2632 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-32-2634         TCGA-32-2638         TCGA-32-4213 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-32-5222         TCGA-41-2571         TCGA-41-2572 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-41-3915         TCGA-41-4097         TCGA-41-5651 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-76-4925         TCGA-76-4926         TCGA-76-4928 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
D19V10, multiclass
[1] "Remove cluster labels:" "10P GAIN CNV"          
clus
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 1                146 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2570         TCGA-06-5408 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-5410         TCGA-06-5411         TCGA-06-5412 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-5413         TCGA-06-5414         TCGA-06-5415 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-5416         TCGA-06-5418         TCGA-06-5856 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-5858         TCGA-06-5859         TCGA-08-0386 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-12-0616         TCGA-12-0618         TCGA-12-0619 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-12-0821         TCGA-12-3650         TCGA-12-3652 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-12-3653         TCGA-12-5295         TCGA-12-5299 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-14-0781         TCGA-14-0787         TCGA-14-0789 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-14-0790         TCGA-14-0817         TCGA-14-1034 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-14-1823         TCGA-14-1825         TCGA-14-1829 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-14-2554         TCGA-15-0742         TCGA-15-1444 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-16-0846         TCGA-16-1045         TCGA-19-1390 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2620 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-19-2624         TCGA-19-2625         TCGA-19-2629 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-19-4065         TCGA-19-5960         TCGA-26-1442 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-26-5135         TCGA-26-5136         TCGA-26-5139 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-27-1830         TCGA-27-1831         TCGA-27-1832 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1835         TCGA-27-1837 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-27-2519         TCGA-27-2521         TCGA-27-2523 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-27-2524         TCGA-27-2526         TCGA-27-2528 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-28-1747         TCGA-28-1753         TCGA-28-2509 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-28-2510         TCGA-28-2513         TCGA-28-2514 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5213         TCGA-28-5215 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-28-5216         TCGA-28-5218         TCGA-28-5220 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-32-1970         TCGA-32-1980         TCGA-32-1982 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-32-2615         TCGA-32-2616         TCGA-32-2632 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-32-2634         TCGA-32-2638         TCGA-32-4213 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-32-5222         TCGA-41-2571         TCGA-41-2572 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-41-3915         TCGA-41-4097         TCGA-41-5651 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-76-4925         TCGA-76-4926         TCGA-76-4928 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 

Clustering(20) Variable = 11p gain
D20V1, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            1                146
  CLUS_2            1                 95
  CLUS_3            1                151
  CLUS_4            0                113
D20V2, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            0                117
  CLUS_2            1                170
  CLUS_3            2                218
D20V3, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            2                137
  CLUS_2            1                154
  CLUS_3            0                 73
  CLUS_4            0                104
D20V4, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            2                179
  CLUS_2            0                155
  CLUS_3            1                134
D20V5, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            0                161
  CLUS_2            3                185
  CLUS_3            1                211
D20V6, multiclass
[1] "Remove cluster labels:" "11P GAIN CNV"          
clus
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 1                108 
        TCGA-06-0650         TCGA-06-1804         TCGA-06-1806 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5299         TCGA-12-5301 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-14-0740         TCGA-14-0781         TCGA-14-0862 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-14-1043         TCGA-14-1395         TCGA-14-1450 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-15-1444         TCGA-19-5947         TCGA-19-5950 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-5951         TCGA-19-5952         TCGA-19-5953 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-5954         TCGA-19-5955         TCGA-19-5956 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-5958         TCGA-19-5959         TCGA-19-5960 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-26-1442         TCGA-26-5132         TCGA-26-5133 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-26-5134         TCGA-26-5135         TCGA-26-5136 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-26-5139         TCGA-26-6173         TCGA-26-6174 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-2501         TCGA-28-2510         TCGA-28-5204 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-5211         TCGA-28-5213         TCGA-28-5214 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-5215         TCGA-28-5216         TCGA-28-5218 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-5219         TCGA-28-5220         TCGA-28-6450 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-1979         TCGA-32-1980         TCGA-32-5222 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-41-5651         TCGA-41-6646         TCGA-74-6573 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-74-6575         TCGA-74-6577         TCGA-74-6578 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-74-6581         TCGA-74-6584         TCGA-76-4925 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-4931         TCGA-76-4934         TCGA-76-4935 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6191         TCGA-76-6192         TCGA-76-6193 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6280         TCGA-76-6282         TCGA-76-6283 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6285         TCGA-76-6286         TCGA-76-6656 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6657         TCGA-76-6660         TCGA-76-6661 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6662         TCGA-76-6663         TCGA-76-6664 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-81-5910         TCGA-81-5911         TCGA-87-5896 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D20V7, multiclass
[1] "Remove cluster labels:" "11P GAIN CNV"          
clus
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 1                200 
        TCGA-02-0003         TCGA-02-0011         TCGA-02-0068 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-02-0069         TCGA-02-0116         TCGA-02-2470 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-06-0125         TCGA-06-0126 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0128         TCGA-06-0129         TCGA-06-0130 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0154         TCGA-06-0155         TCGA-06-0171 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0189         TCGA-06-0238         TCGA-06-0644 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0650         TCGA-06-0875         TCGA-06-0876 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0877         TCGA-06-0878         TCGA-06-0879 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0882         TCGA-06-0939         TCGA-06-1084 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-1086         TCGA-06-1087         TCGA-06-1800 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-1802         TCGA-06-1804         TCGA-06-1805 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-1806         TCGA-06-2557         TCGA-06-2558 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2562         TCGA-06-2563 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-2564         TCGA-06-2565         TCGA-06-2566 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2570         TCGA-06-5408 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5410         TCGA-06-5411         TCGA-06-5412 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5413         TCGA-06-5414         TCGA-06-5415 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5416         TCGA-06-5418         TCGA-06-5856 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5858         TCGA-06-5859         TCGA-06-6388 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-6389         TCGA-06-6390         TCGA-06-6391 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-6693         TCGA-06-6694         TCGA-06-6695 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-6697         TCGA-06-6698         TCGA-06-6699 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-6700         TCGA-06-6701         TCGA-08-0245 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0344         TCGA-08-0345         TCGA-08-0346 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0347         TCGA-08-0348         TCGA-08-0349 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0350         TCGA-08-0351         TCGA-08-0352 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0353         TCGA-08-0354         TCGA-08-0355 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0356         TCGA-08-0357         TCGA-08-0358 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0359         TCGA-08-0375         TCGA-08-0380 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0386         TCGA-08-0389         TCGA-08-0390 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0392         TCGA-12-0691         TCGA-12-0692 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-1598         TCGA-12-1599         TCGA-12-3646 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-3649         TCGA-12-3650         TCGA-12-3651 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-5301         TCGA-14-0813         TCGA-14-0862 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-14-0871         TCGA-14-1823         TCGA-15-1446 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-15-1447         TCGA-15-1449         TCGA-16-0846 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-16-1460         TCGA-19-0957         TCGA-19-0962 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-1386         TCGA-19-1389         TCGA-19-1390 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-1392         TCGA-19-1786         TCGA-19-1789 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-1791         TCGA-19-2619         TCGA-19-2620 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-2625         TCGA-19-2631         TCGA-19-5947 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-5950         TCGA-19-5951         TCGA-19-5952 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-5953         TCGA-19-5954         TCGA-19-5955 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-5956         TCGA-19-5958         TCGA-19-5959 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1440         TCGA-26-1442 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-26-6173         TCGA-26-6174         TCGA-27-1830 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1833 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1836         TCGA-27-2518 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-2528         TCGA-28-1746         TCGA-28-1747 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-1750         TCGA-28-1752         TCGA-28-1753 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-1757         TCGA-28-2501         TCGA-28-5208 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-5214         TCGA-32-1970         TCGA-32-1976 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-1978         TCGA-32-1982         TCGA-32-1986 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-1987         TCGA-32-1991         TCGA-32-4210 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-4211         TCGA-32-5222         TCGA-41-2573 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-41-2575         TCGA-41-3392         TCGA-41-3393 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-41-3915         TCGA-41-4097         TCGA-41-5651 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-41-6646         TCGA-74-6573         TCGA-74-6575 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-74-6577         TCGA-74-6578         TCGA-74-6581 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-74-6584         TCGA-76-4926         TCGA-76-4928 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931         TCGA-76-6192 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6193         TCGA-76-6282         TCGA-76-6283 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6285         TCGA-76-6656         TCGA-76-6657 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6660         TCGA-76-6662         TCGA-76-6663 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6664         TCGA-81-5910 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D20V8, multiclass
[1] "Remove cluster labels:" "11P GAIN CNV"          
clus
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 1                200 
        TCGA-02-0003         TCGA-02-0011         TCGA-02-0068 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-02-0069         TCGA-02-0116         TCGA-02-2470 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-06-0125         TCGA-06-0126 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0128         TCGA-06-0129         TCGA-06-0130 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0154         TCGA-06-0155         TCGA-06-0171 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0189         TCGA-06-0238         TCGA-06-0644 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0650         TCGA-06-0875         TCGA-06-0876 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0877         TCGA-06-0878         TCGA-06-0879 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0882         TCGA-06-0939         TCGA-06-1084 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-1086         TCGA-06-1087         TCGA-06-1800 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-1802         TCGA-06-1804         TCGA-06-1805 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-1806         TCGA-06-2557         TCGA-06-2558 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2562         TCGA-06-2563 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-2564         TCGA-06-2565         TCGA-06-2566 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2570         TCGA-06-5408 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5410         TCGA-06-5411         TCGA-06-5412 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5413         TCGA-06-5414         TCGA-06-5415 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5416         TCGA-06-5418         TCGA-06-5856 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5858         TCGA-06-5859         TCGA-06-6388 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-6389         TCGA-06-6390         TCGA-06-6391 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-6693         TCGA-06-6694         TCGA-06-6695 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-6697         TCGA-06-6698         TCGA-06-6699 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-6700         TCGA-06-6701         TCGA-08-0245 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0344         TCGA-08-0345         TCGA-08-0346 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0347         TCGA-08-0348         TCGA-08-0349 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0350         TCGA-08-0351         TCGA-08-0352 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0353         TCGA-08-0354         TCGA-08-0355 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0356         TCGA-08-0357         TCGA-08-0358 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0359         TCGA-08-0375         TCGA-08-0380 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0386         TCGA-08-0389         TCGA-08-0390 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0392         TCGA-12-0691         TCGA-12-0692 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-1598         TCGA-12-1599         TCGA-12-3646 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-3649         TCGA-12-3650         TCGA-12-3651 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-5301         TCGA-14-0813         TCGA-14-0862 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-14-0871         TCGA-14-1823         TCGA-15-1446 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-15-1447         TCGA-15-1449         TCGA-16-0846 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-16-1460         TCGA-19-0957         TCGA-19-0962 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-1386         TCGA-19-1389         TCGA-19-1390 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-1392         TCGA-19-1786         TCGA-19-1789 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-1791         TCGA-19-2619         TCGA-19-2620 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-2625         TCGA-19-2631         TCGA-19-5947 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-5950         TCGA-19-5951         TCGA-19-5952 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-5953         TCGA-19-5954         TCGA-19-5955 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-5956         TCGA-19-5958         TCGA-19-5959 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1440         TCGA-26-1442 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-26-6173         TCGA-26-6174         TCGA-27-1830 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1833 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1836         TCGA-27-2518 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-2528         TCGA-28-1746         TCGA-28-1747 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-1750         TCGA-28-1752         TCGA-28-1753 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-1757         TCGA-28-2501         TCGA-28-5208 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-5214         TCGA-32-1970         TCGA-32-1976 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-1978         TCGA-32-1982         TCGA-32-1986 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-1987         TCGA-32-1991         TCGA-32-4210 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-4211         TCGA-32-5222         TCGA-41-2573 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-41-2575         TCGA-41-3392         TCGA-41-3393 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-41-3915         TCGA-41-4097         TCGA-41-5651 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-41-6646         TCGA-74-6573         TCGA-74-6575 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-74-6577         TCGA-74-6578         TCGA-74-6581 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-74-6584         TCGA-76-4926         TCGA-76-4928 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931         TCGA-76-6192 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6193         TCGA-76-6282         TCGA-76-6283 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6285         TCGA-76-6656         TCGA-76-6657 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6660         TCGA-76-6662         TCGA-76-6663 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6664         TCGA-81-5910 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D20V9, multiclass
[1] "Remove cluster labels:" "11P GAIN CNV"          
clus
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2569         TCGA-06-2570 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0386         TCGA-12-0616         TCGA-12-0618 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-0619         TCGA-12-0821         TCGA-12-3650 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-5299         TCGA-14-0781         TCGA-14-0787 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-14-0789         TCGA-14-0790         TCGA-14-0817 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-14-1034         TCGA-14-1823         TCGA-14-1825 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-14-1829         TCGA-14-2554         TCGA-15-0742 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-15-1444         TCGA-16-0846         TCGA-16-1045 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-1390         TCGA-19-1787         TCGA-19-2619 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-2620         TCGA-19-2624         TCGA-19-2625 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-2629         TCGA-19-5960         TCGA-26-1442 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-26-5135         TCGA-26-5136         TCGA-26-5139 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-1830         TCGA-27-1831         TCGA-27-1832 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1835         TCGA-27-1837 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-2519         TCGA-27-2521         TCGA-27-2523 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-2524         TCGA-27-2528         TCGA-28-1747 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-1753         TCGA-28-2509         TCGA-28-2510 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-2513         TCGA-28-2514         TCGA-28-5204 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-5213         TCGA-28-5215         TCGA-28-5216 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-5218         TCGA-28-5220         TCGA-32-1970 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-4931 
"11P GAIN WILD-TYPE" 
D20V10, multiclass
[1] "Remove cluster labels:" "11P GAIN CNV"          
clus
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2569         TCGA-06-2570 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0386         TCGA-12-0616         TCGA-12-0618 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-0619         TCGA-12-0821         TCGA-12-3650 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-5299         TCGA-14-0781         TCGA-14-0787 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-14-0789         TCGA-14-0790         TCGA-14-0817 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-14-1034         TCGA-14-1823         TCGA-14-1825 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-14-1829         TCGA-14-2554         TCGA-15-0742 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-15-1444         TCGA-16-0846         TCGA-16-1045 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-1390         TCGA-19-1787         TCGA-19-2619 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-2620         TCGA-19-2624         TCGA-19-2625 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-2629         TCGA-19-5960         TCGA-26-1442 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-26-5135         TCGA-26-5136         TCGA-26-5139 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-1830         TCGA-27-1831         TCGA-27-1832 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1835         TCGA-27-1837 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-2519         TCGA-27-2521         TCGA-27-2523 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-2524         TCGA-27-2528         TCGA-28-1747 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-1753         TCGA-28-2509         TCGA-28-2510 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-2513         TCGA-28-2514         TCGA-28-5204 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-5213         TCGA-28-5215         TCGA-28-5216 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-5218         TCGA-28-5220         TCGA-32-1970 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-4931 
"11P GAIN WILD-TYPE" 

Clustering(21) Variable = 11q gain
D21V1, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            1                146
  CLUS_2            3                 93
  CLUS_3            0                152
  CLUS_4            2                111
D21V2, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            0                117
  CLUS_2            4                167
  CLUS_3            2                218
D21V3, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            0                139
  CLUS_2            3                152
  CLUS_3            0                 73
  CLUS_4            2                102
D21V4, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            0                181
  CLUS_2            2                153
  CLUS_3            3                132
D21V5, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            1                160
  CLUS_2            5                183
  CLUS_3            1                211
D21V6, multiclass
[1] "Remove cluster labels:" "11Q GAIN CNV"          
clus
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 1                108 
        TCGA-06-0650         TCGA-06-1804         TCGA-06-1806 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5299         TCGA-12-5301 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-14-0740         TCGA-14-0781         TCGA-14-0862 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-14-1043         TCGA-14-1395         TCGA-14-1450 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-15-1444         TCGA-19-5947         TCGA-19-5950 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-19-5951         TCGA-19-5952         TCGA-19-5953 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-19-5954         TCGA-19-5955         TCGA-19-5956 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-19-5958         TCGA-19-5959         TCGA-19-5960 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-26-1442         TCGA-26-5132         TCGA-26-5133 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-26-5134         TCGA-26-5135         TCGA-26-5136 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-26-5139         TCGA-26-6173         TCGA-26-6174 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-2501         TCGA-28-2510         TCGA-28-5204 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-5211         TCGA-28-5213         TCGA-28-5214 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-5215         TCGA-28-5216         TCGA-28-5218 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-5219         TCGA-28-5220         TCGA-28-6450 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-32-1979         TCGA-32-1980         TCGA-32-5222 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-41-5651         TCGA-41-6646         TCGA-74-6573 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-74-6575         TCGA-74-6577         TCGA-74-6578 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-74-6581         TCGA-74-6584         TCGA-76-4925 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-76-4931         TCGA-76-4934         TCGA-76-4935 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-76-6191         TCGA-76-6192         TCGA-76-6193 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-76-6280         TCGA-76-6282         TCGA-76-6283 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-76-6285         TCGA-76-6286         TCGA-76-6656 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-76-6657         TCGA-76-6660         TCGA-76-6661 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-76-6662         TCGA-76-6663         TCGA-76-6664 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-81-5910         TCGA-81-5911         TCGA-87-5896 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D21V7, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            1                 53
  CLUS_2            1                 57
  CLUS_3            0                 44
  CLUS_4            1                 44
D21V8, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            0                 64
  CLUS_2            0                 33
  CLUS_3            3                101
D21V9, multiclass
[1] "Remove cluster labels:" "11Q GAIN CNV"          
clus
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 1                146 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2569         TCGA-06-2570 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-08-0386         TCGA-12-0616         TCGA-12-0618 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-12-0619         TCGA-12-0821         TCGA-12-3650 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-12-5299         TCGA-14-0781         TCGA-14-0787 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-14-0789         TCGA-14-0790         TCGA-14-0817 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-14-1034         TCGA-14-1823         TCGA-14-1825 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-14-1829         TCGA-14-2554         TCGA-15-0742 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-15-1444         TCGA-16-0846         TCGA-16-1045 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-19-1390         TCGA-19-1787         TCGA-19-2619 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-19-2620         TCGA-19-2624         TCGA-19-2625 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-19-2629         TCGA-19-5960         TCGA-26-1442 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-26-5135         TCGA-26-5136         TCGA-26-5139 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-27-1830         TCGA-27-1831         TCGA-27-1832 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1835         TCGA-27-1837 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-27-2519         TCGA-27-2521         TCGA-27-2523 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-27-2524         TCGA-27-2526         TCGA-27-2528 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-1747         TCGA-28-1753         TCGA-28-2509 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-2510         TCGA-28-2513         TCGA-28-2514 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5213         TCGA-28-5215 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-5216         TCGA-28-5218         TCGA-28-5220 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-32-1970         TCGA-32-1980         TCGA-32-1982 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-32-2615         TCGA-32-2616         TCGA-32-2632 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-32-2634         TCGA-32-2638         TCGA-32-4213 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-32-5222         TCGA-41-2571         TCGA-41-2572 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-41-3915         TCGA-41-4097         TCGA-41-5651 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-76-4925         TCGA-76-4926         TCGA-76-4928 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D21V10, multiclass
[1] "Remove cluster labels:" "11Q GAIN CNV"          
clus
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 1                146 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2569         TCGA-06-2570 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-08-0386         TCGA-12-0616         TCGA-12-0618 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-12-0619         TCGA-12-0821         TCGA-12-3650 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-12-5299         TCGA-14-0781         TCGA-14-0787 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-14-0789         TCGA-14-0790         TCGA-14-0817 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-14-1034         TCGA-14-1823         TCGA-14-1825 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-14-1829         TCGA-14-2554         TCGA-15-0742 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-15-1444         TCGA-16-0846         TCGA-16-1045 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-19-1390         TCGA-19-1787         TCGA-19-2619 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-19-2620         TCGA-19-2624         TCGA-19-2625 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-19-2629         TCGA-19-5960         TCGA-26-1442 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-26-5135         TCGA-26-5136         TCGA-26-5139 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-27-1830         TCGA-27-1831         TCGA-27-1832 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1835         TCGA-27-1837 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-27-2519         TCGA-27-2521         TCGA-27-2523 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-27-2524         TCGA-27-2526         TCGA-27-2528 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-1747         TCGA-28-1753         TCGA-28-2509 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-2510         TCGA-28-2513         TCGA-28-2514 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5213         TCGA-28-5215 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-5216         TCGA-28-5218         TCGA-28-5220 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-32-1970         TCGA-32-1980         TCGA-32-1982 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-32-2615         TCGA-32-2616         TCGA-32-2632 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-32-2634         TCGA-32-2638         TCGA-32-4213 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-32-5222         TCGA-41-2571         TCGA-41-2572 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-41-3915         TCGA-41-4097         TCGA-41-5651 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-76-4925         TCGA-76-4926         TCGA-76-4928 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 

Clustering(22) Variable = 12p gain
D22V1, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           10                137
  CLUS_2           10                 86
  CLUS_3           10                142
  CLUS_4            7                106
D22V2, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            9                108
  CLUS_2            9                162
  CLUS_3           19                201
D22V3, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           10                129
  CLUS_2           13                142
  CLUS_3            7                 66
  CLUS_4            8                 96
D22V4, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           19                162
  CLUS_2           12                143
  CLUS_3            7                128
D22V5, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           22                139
  CLUS_2           11                177
  CLUS_3            9                203
D22V6, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            1                 38
  CLUS_2            2                 25
  CLUS_3            1                 15
  CLUS_4            3                 24
D22V7, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            1                 53
  CLUS_2            5                 53
  CLUS_3            3                 41
  CLUS_4            4                 41
D22V8, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            4                 60
  CLUS_2            1                 32
  CLUS_3            8                 96
D22V9, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            0                 44
  CLUS_2            8                 59
  CLUS_3            2                 34
D22V10, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            7                 59
  CLUS_2            1                 20
  CLUS_3            2                 58

Clustering(23) Variable = 12q gain
D23V1, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            9                138
  CLUS_2            8                 88
  CLUS_3            8                144
  CLUS_4            3                110
D23V2, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            8                109
  CLUS_2            5                166
  CLUS_3           15                205
D23V3, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            7                132
  CLUS_2           11                144
  CLUS_3            5                 68
  CLUS_4            7                 97
D23V4, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1           16                165
  CLUS_2           10                145
  CLUS_3            4                131
D23V5, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1           17                144
  CLUS_2            6                182
  CLUS_3            9                203
D23V6, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            1                 38
  CLUS_2            2                 25
  CLUS_3            1                 15
  CLUS_4            1                 26
D23V7, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            1                 53
  CLUS_2            4                 54
  CLUS_3            3                 41
  CLUS_4            3                 42
D23V8, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            5                 59
  CLUS_2            1                 32
  CLUS_3            5                 99
D23V9, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            0                 44
  CLUS_2            6                 61
  CLUS_3            2                 34
D23V10, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            5                 61
  CLUS_2            1                 20
  CLUS_3            2                 58

Clustering(24) Variable = 13q gain
D24V1, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            1                146
  CLUS_2            2                 94
  CLUS_3            0                152
  CLUS_4            0                113
D24V2, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            0                117
  CLUS_2            1                170
  CLUS_3            2                218
D24V3, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            0                139
  CLUS_2            3                152
  CLUS_3            0                 73
  CLUS_4            0                104
D24V4, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            2                179
  CLUS_2            0                155
  CLUS_3            1                134
D24V5, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            2                159
  CLUS_2            0                188
  CLUS_3            1                211
D24V6, multiclass
[1] "Remove cluster labels:" "13Q GAIN CNV"          
clus
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                 1                108 
        TCGA-06-0650         TCGA-06-1804         TCGA-06-1806 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5299         TCGA-12-5301 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-14-0740         TCGA-14-0781         TCGA-14-0862 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-14-1043         TCGA-14-1395         TCGA-14-1450 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-15-1444         TCGA-19-4065         TCGA-19-5947 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-5950         TCGA-19-5951         TCGA-19-5952 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-5953         TCGA-19-5954         TCGA-19-5955 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-5956         TCGA-19-5958         TCGA-19-5959 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-26-5139         TCGA-26-6173         TCGA-26-6174 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-28-2501         TCGA-28-2510         TCGA-28-5204 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-28-5211         TCGA-28-5213         TCGA-28-5214 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-28-5215         TCGA-28-5216         TCGA-28-5218 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-28-5219         TCGA-28-5220         TCGA-28-6450 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-32-1979         TCGA-32-1980         TCGA-32-5222 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-41-5651         TCGA-41-6646         TCGA-74-6573 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-74-6575         TCGA-74-6577         TCGA-74-6578 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-74-6581         TCGA-74-6584         TCGA-76-4925 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-4931         TCGA-76-4934         TCGA-76-4935 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6191         TCGA-76-6192         TCGA-76-6193 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6280         TCGA-76-6282         TCGA-76-6283 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6285         TCGA-76-6286         TCGA-76-6656 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6657         TCGA-76-6660         TCGA-76-6661 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6662         TCGA-76-6663         TCGA-76-6664 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-81-5910         TCGA-81-5911         TCGA-87-5896 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D24V7, multiclass
[1] "Remove cluster labels:" "13Q GAIN CNV"          
clus
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                 1                200 
        TCGA-02-0003         TCGA-02-0011         TCGA-02-0014 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-02-0068         TCGA-02-0069         TCGA-02-0116 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-02-2470         TCGA-02-2485         TCGA-06-0125 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-0126         TCGA-06-0128         TCGA-06-0129 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-0130         TCGA-06-0154         TCGA-06-0155 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-0171         TCGA-06-0189         TCGA-06-0238 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-0644         TCGA-06-0650         TCGA-06-0875 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-0876         TCGA-06-0877         TCGA-06-0878 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-0879         TCGA-06-0882         TCGA-06-0939 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-1084         TCGA-06-1086         TCGA-06-1087 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-1800         TCGA-06-1802         TCGA-06-1804 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-1805         TCGA-06-1806         TCGA-06-2557 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-2558         TCGA-06-2559         TCGA-06-2562 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-2566         TCGA-06-2567         TCGA-06-2570 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0245         TCGA-08-0344         TCGA-08-0345 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0346         TCGA-08-0347         TCGA-08-0348 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0349         TCGA-08-0350         TCGA-08-0351 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0352         TCGA-08-0353         TCGA-08-0354 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0355         TCGA-08-0356         TCGA-08-0357 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0358         TCGA-08-0359         TCGA-08-0375 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0380         TCGA-08-0386         TCGA-08-0389 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0390         TCGA-08-0392         TCGA-12-0691 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-12-0692         TCGA-12-1598         TCGA-12-1599 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-12-3646         TCGA-12-3649         TCGA-12-3650 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-12-3651         TCGA-12-3652         TCGA-12-3653 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5301         TCGA-14-0813 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-14-0862         TCGA-14-0871         TCGA-14-1823 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-15-1446         TCGA-15-1447         TCGA-15-1449 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-16-0846         TCGA-16-1460         TCGA-19-0957 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-0962         TCGA-19-1386         TCGA-19-1389 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-1392         TCGA-19-1786         TCGA-19-1789 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-1791         TCGA-19-2619         TCGA-19-2620 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-2625         TCGA-19-2631         TCGA-19-5947 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-5950         TCGA-19-5951         TCGA-19-5952 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-5953         TCGA-19-5954         TCGA-19-5955 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-5956         TCGA-19-5958         TCGA-19-5959 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1440         TCGA-26-1442 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-26-6173         TCGA-26-6174         TCGA-27-1830 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1833 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1836         TCGA-27-2518 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-27-2528         TCGA-28-1746         TCGA-28-1747 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-28-1750         TCGA-28-1752         TCGA-28-1753 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-28-1757         TCGA-28-2501         TCGA-28-5208 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-28-5214         TCGA-32-1970         TCGA-32-1976 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-32-1978         TCGA-32-1982         TCGA-32-1986 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-32-1987         TCGA-32-1991         TCGA-32-4210 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-32-4211         TCGA-32-5222         TCGA-41-2573 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-41-2575         TCGA-41-3392         TCGA-41-3393 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-41-3915         TCGA-41-4097         TCGA-41-5651 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-41-6646         TCGA-74-6573         TCGA-74-6575 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-74-6577         TCGA-74-6578         TCGA-74-6581 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-74-6584         TCGA-76-4926         TCGA-76-4928 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931         TCGA-76-6192 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6193         TCGA-76-6282         TCGA-76-6283 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6285         TCGA-76-6656         TCGA-76-6657 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6660         TCGA-76-6662         TCGA-76-6663 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6664         TCGA-81-5910 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D24V8, multiclass
[1] "Remove cluster labels:" "13Q GAIN CNV"          
clus
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                 1                200 
        TCGA-02-0003         TCGA-02-0011         TCGA-02-0014 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-02-0068         TCGA-02-0069         TCGA-02-0116 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-02-2470         TCGA-02-2485         TCGA-06-0125 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-0126         TCGA-06-0128         TCGA-06-0129 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-0130         TCGA-06-0154         TCGA-06-0155 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-0171         TCGA-06-0189         TCGA-06-0238 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-0644         TCGA-06-0650         TCGA-06-0875 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-0876         TCGA-06-0877         TCGA-06-0878 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-0879         TCGA-06-0882         TCGA-06-0939 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-1084         TCGA-06-1086         TCGA-06-1087 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-1800         TCGA-06-1802         TCGA-06-1804 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-1805         TCGA-06-1806         TCGA-06-2557 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-2558         TCGA-06-2559         TCGA-06-2562 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-2566         TCGA-06-2567         TCGA-06-2570 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0245         TCGA-08-0344         TCGA-08-0345 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0346         TCGA-08-0347         TCGA-08-0348 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0349         TCGA-08-0350         TCGA-08-0351 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0352         TCGA-08-0353         TCGA-08-0354 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0355         TCGA-08-0356         TCGA-08-0357 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0358         TCGA-08-0359         TCGA-08-0375 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0380         TCGA-08-0386         TCGA-08-0389 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0390         TCGA-08-0392         TCGA-12-0691 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-12-0692         TCGA-12-1598         TCGA-12-1599 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-12-3646         TCGA-12-3649         TCGA-12-3650 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-12-3651         TCGA-12-3652         TCGA-12-3653 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5301         TCGA-14-0813 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-14-0862         TCGA-14-0871         TCGA-14-1823 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-15-1446         TCGA-15-1447         TCGA-15-1449 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-16-0846         TCGA-16-1460         TCGA-19-0957 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-0962         TCGA-19-1386         TCGA-19-1389 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-1392         TCGA-19-1786         TCGA-19-1789 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-1791         TCGA-19-2619         TCGA-19-2620 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-2625         TCGA-19-2631         TCGA-19-5947 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-5950         TCGA-19-5951         TCGA-19-5952 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-5953         TCGA-19-5954         TCGA-19-5955 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-5956         TCGA-19-5958         TCGA-19-5959 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1440         TCGA-26-1442 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-26-6173         TCGA-26-6174         TCGA-27-1830 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1833 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1836         TCGA-27-2518 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-27-2528         TCGA-28-1746         TCGA-28-1747 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-28-1750         TCGA-28-1752         TCGA-28-1753 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-28-1757         TCGA-28-2501         TCGA-28-5208 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-28-5214         TCGA-32-1970         TCGA-32-1976 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-32-1978         TCGA-32-1982         TCGA-32-1986 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-32-1987         TCGA-32-1991         TCGA-32-4210 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-32-4211         TCGA-32-5222         TCGA-41-2573 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-41-2575         TCGA-41-3392         TCGA-41-3393 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-41-3915         TCGA-41-4097         TCGA-41-5651 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-41-6646         TCGA-74-6573         TCGA-74-6575 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-74-6577         TCGA-74-6578         TCGA-74-6581 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-74-6584         TCGA-76-4926         TCGA-76-4928 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931         TCGA-76-6192 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6193         TCGA-76-6282         TCGA-76-6283 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6285         TCGA-76-6656         TCGA-76-6657 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6660         TCGA-76-6662         TCGA-76-6663 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6664         TCGA-81-5910 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D24V9, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            1                 43
  CLUS_2            1                 66
  CLUS_3            1                 35
D24V10, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            1                 65
  CLUS_2            1                 20
  CLUS_3            1                 59

Clustering(25) Variable = 14q gain
D25V1, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            3                144
  CLUS_2            1                 95
  CLUS_3            2                150
  CLUS_4            0                113
D25V2, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            1                116
  CLUS_2            0                171
  CLUS_3            5                215
D25V3, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            5                134
  CLUS_2            0                155
  CLUS_3            1                 72
  CLUS_4            1                103
D25V4, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            2                179
  CLUS_2            4                151
  CLUS_3            1                134
D25V5, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            1                160
  CLUS_2            2                186
  CLUS_3            4                208
D25V6, multiclass
D25V7, multiclass
D25V8, multiclass
D25V9, multiclass
[1] "Remove cluster labels:" "14Q GAIN CNV"          
clus
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2570         TCGA-06-5408 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-5410         TCGA-06-5411         TCGA-06-5412 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-5413         TCGA-06-5414         TCGA-06-5415 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-5416         TCGA-06-5418         TCGA-06-5856 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-5858         TCGA-06-5859         TCGA-08-0386 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-12-0616         TCGA-12-0618         TCGA-12-0619 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-12-0821         TCGA-12-3650         TCGA-12-3652 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-12-3653         TCGA-12-5295         TCGA-12-5299 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-14-0781         TCGA-14-0787         TCGA-14-0789 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-14-0790         TCGA-14-0817         TCGA-14-1034 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-14-1823         TCGA-14-1825         TCGA-14-1829 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-14-2554         TCGA-15-0742         TCGA-15-1444 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-16-0846         TCGA-16-1045         TCGA-19-1390 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2620 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-19-2624         TCGA-19-2625         TCGA-19-2629 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-19-4065         TCGA-19-5960         TCGA-26-1442 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-26-5135         TCGA-26-5136         TCGA-26-5139 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-27-1830         TCGA-27-1831         TCGA-27-1832 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1835         TCGA-27-1837 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-27-2519         TCGA-27-2521         TCGA-27-2523 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-27-2524         TCGA-27-2526         TCGA-27-2528 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-28-1747         TCGA-28-1753         TCGA-28-2509 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-28-2510         TCGA-28-2513         TCGA-28-2514 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5213         TCGA-28-5215 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-28-5216         TCGA-28-5218         TCGA-28-5220 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-32-1970         TCGA-32-1980         TCGA-32-1982 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-32-2615         TCGA-32-2616         TCGA-32-2634 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-76-4931 
"14Q GAIN WILD-TYPE" 
D25V10, multiclass
[1] "Remove cluster labels:" "14Q GAIN CNV"          
clus
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2570         TCGA-06-5408 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-5410         TCGA-06-5411         TCGA-06-5412 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-5413         TCGA-06-5414         TCGA-06-5415 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-5416         TCGA-06-5418         TCGA-06-5856 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-5858         TCGA-06-5859         TCGA-08-0386 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-12-0616         TCGA-12-0618         TCGA-12-0619 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-12-0821         TCGA-12-3650         TCGA-12-3652 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-12-3653         TCGA-12-5295         TCGA-12-5299 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-14-0781         TCGA-14-0787         TCGA-14-0789 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-14-0790         TCGA-14-0817         TCGA-14-1034 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-14-1823         TCGA-14-1825         TCGA-14-1829 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-14-2554         TCGA-15-0742         TCGA-15-1444 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-16-0846         TCGA-16-1045         TCGA-19-1390 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2620 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-19-2624         TCGA-19-2625         TCGA-19-2629 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-19-4065         TCGA-19-5960         TCGA-26-1442 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-26-5135         TCGA-26-5136         TCGA-26-5139 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-27-1830         TCGA-27-1831         TCGA-27-1832 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1835         TCGA-27-1837 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-27-2519         TCGA-27-2521         TCGA-27-2523 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-27-2524         TCGA-27-2526         TCGA-27-2528 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-28-1747         TCGA-28-1753         TCGA-28-2509 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-28-2510         TCGA-28-2513         TCGA-28-2514 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5213         TCGA-28-5215 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-28-5216         TCGA-28-5218         TCGA-28-5220 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-32-1970         TCGA-32-1980         TCGA-32-1982 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-32-2615         TCGA-32-2616         TCGA-32-2634 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-76-4931 
"14Q GAIN WILD-TYPE" 

Clustering(26) Variable = 15q gain
D26V1, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            2                145
  CLUS_2            2                 94
  CLUS_3            0                152
  CLUS_4            1                112
D26V2, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            0                117
  CLUS_2            2                169
  CLUS_3            3                217
D26V3, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            3                136
  CLUS_2            1                154
  CLUS_3            0                 73
  CLUS_4            2                102
D26V4, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            1                180
  CLUS_2            3                152
  CLUS_3            2                133
D26V5, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            5                156
  CLUS_2            0                188
  CLUS_3            1                211
D26V6, multiclass
[1] "Remove cluster labels:" "15Q GAIN CNV"          
clus
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 1                108 
        TCGA-06-0650         TCGA-06-1804         TCGA-06-1806 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5299         TCGA-12-5301 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-14-0740         TCGA-14-0781         TCGA-14-0862 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-14-1043         TCGA-14-1395         TCGA-14-1450 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-15-1444         TCGA-19-4065         TCGA-19-5947 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-5950         TCGA-19-5951         TCGA-19-5952 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-5953         TCGA-19-5954         TCGA-19-5955 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-5956         TCGA-19-5958         TCGA-19-5959 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-26-5136         TCGA-26-5139         TCGA-26-6173 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-26-6174         TCGA-28-2501         TCGA-28-2510 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5211         TCGA-28-5213 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-5214         TCGA-28-5215         TCGA-28-5216 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-5219         TCGA-28-5220         TCGA-28-6450 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-1979         TCGA-32-1980         TCGA-32-5222 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-41-5651         TCGA-41-6646         TCGA-74-6573 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-74-6575         TCGA-74-6577         TCGA-74-6578 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-74-6581         TCGA-74-6584         TCGA-76-4925 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-4931         TCGA-76-4934         TCGA-76-4935 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6191         TCGA-76-6192         TCGA-76-6193 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6280         TCGA-76-6282         TCGA-76-6283 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6285         TCGA-76-6286         TCGA-76-6656 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6657         TCGA-76-6660         TCGA-76-6661 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6662         TCGA-76-6663         TCGA-76-6664 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-81-5910         TCGA-81-5911         TCGA-87-5896 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
D26V7, multiclass
[1] "Remove cluster labels:" "15Q GAIN CNV"          
clus
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 1                200 
        TCGA-02-0003         TCGA-02-0011         TCGA-02-0014 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-02-0068         TCGA-02-0069         TCGA-02-0116 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-02-2470         TCGA-02-2485         TCGA-06-0125 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0126         TCGA-06-0128         TCGA-06-0129 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0130         TCGA-06-0154         TCGA-06-0155 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0171         TCGA-06-0189         TCGA-06-0238 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0644         TCGA-06-0650         TCGA-06-0875 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0876         TCGA-06-0877         TCGA-06-0878 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0879         TCGA-06-0882         TCGA-06-0939 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-1084         TCGA-06-1086         TCGA-06-1087 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-1800         TCGA-06-1802         TCGA-06-1804 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-1805         TCGA-06-1806         TCGA-06-2557 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-2558         TCGA-06-2559         TCGA-06-2562 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-2566         TCGA-06-2567         TCGA-06-2570 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0245         TCGA-08-0344         TCGA-08-0345 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0346         TCGA-08-0347         TCGA-08-0348 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0349         TCGA-08-0350         TCGA-08-0351 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0352         TCGA-08-0353         TCGA-08-0354 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0355         TCGA-08-0356         TCGA-08-0357 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0358         TCGA-08-0359         TCGA-08-0375 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0380         TCGA-08-0386         TCGA-08-0389 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0390         TCGA-08-0392         TCGA-12-0691 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-0692         TCGA-12-1598         TCGA-12-1599 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-3646         TCGA-12-3649         TCGA-12-3650 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-3651         TCGA-12-3652         TCGA-12-3653 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5301         TCGA-14-0813 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-14-0862         TCGA-14-0871         TCGA-15-1446 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-15-1447         TCGA-15-1449         TCGA-16-0846 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-16-1460         TCGA-19-0957         TCGA-19-0962 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-1386         TCGA-19-1389         TCGA-19-1390 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-1392         TCGA-19-1786         TCGA-19-1789 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-1791         TCGA-19-2619         TCGA-19-2620 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-2625         TCGA-19-2631         TCGA-19-5947 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-5950         TCGA-19-5951         TCGA-19-5952 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-5953         TCGA-19-5954         TCGA-19-5955 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-5956         TCGA-19-5958         TCGA-19-5959 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1440         TCGA-26-1442 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-26-6173         TCGA-26-6174         TCGA-27-1830 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1833 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1836         TCGA-27-2518 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-2528         TCGA-28-1746         TCGA-28-1747 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-1750         TCGA-28-1752         TCGA-28-1753 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-1757         TCGA-28-2501         TCGA-28-5208 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-5214         TCGA-32-1970         TCGA-32-1976 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-1978         TCGA-32-1982         TCGA-32-1986 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-1987         TCGA-32-1991         TCGA-32-4210 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-4211         TCGA-32-5222         TCGA-41-2573 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-41-2575         TCGA-41-3392         TCGA-41-3393 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-41-3915         TCGA-41-4097         TCGA-41-5651 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-41-6646         TCGA-74-6573         TCGA-74-6575 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-74-6577         TCGA-74-6578         TCGA-74-6581 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-74-6584         TCGA-76-4926         TCGA-76-4928 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931         TCGA-76-6192 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6193         TCGA-76-6282         TCGA-76-6283 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6285         TCGA-76-6656         TCGA-76-6657 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6660         TCGA-76-6662         TCGA-76-6663 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6664         TCGA-81-5910 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
D26V8, multiclass
[1] "Remove cluster labels:" "15Q GAIN CNV"          
clus
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 1                200 
        TCGA-02-0003         TCGA-02-0011         TCGA-02-0014 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-02-0068         TCGA-02-0069         TCGA-02-0116 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-02-2470         TCGA-02-2485         TCGA-06-0125 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0126         TCGA-06-0128         TCGA-06-0129 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0130         TCGA-06-0154         TCGA-06-0155 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0171         TCGA-06-0189         TCGA-06-0238 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0644         TCGA-06-0650         TCGA-06-0875 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0876         TCGA-06-0877         TCGA-06-0878 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0879         TCGA-06-0882         TCGA-06-0939 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-1084         TCGA-06-1086         TCGA-06-1087 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-1800         TCGA-06-1802         TCGA-06-1804 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-1805         TCGA-06-1806         TCGA-06-2557 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-2558         TCGA-06-2559         TCGA-06-2562 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-2566         TCGA-06-2567         TCGA-06-2570 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0245         TCGA-08-0344         TCGA-08-0345 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0346         TCGA-08-0347         TCGA-08-0348 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0349         TCGA-08-0350         TCGA-08-0351 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0352         TCGA-08-0353         TCGA-08-0354 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0355         TCGA-08-0356         TCGA-08-0357 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0358         TCGA-08-0359         TCGA-08-0375 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0380         TCGA-08-0386         TCGA-08-0389 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0390         TCGA-08-0392         TCGA-12-0691 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-0692         TCGA-12-1598         TCGA-12-1599 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-3646         TCGA-12-3649         TCGA-12-3650 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-3651         TCGA-12-3652         TCGA-12-3653 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5301         TCGA-14-0813 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-14-0862         TCGA-14-0871         TCGA-15-1446 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-15-1447         TCGA-15-1449         TCGA-16-0846 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-16-1460         TCGA-19-0957         TCGA-19-0962 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-1386         TCGA-19-1389         TCGA-19-1390 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-1392         TCGA-19-1786         TCGA-19-1789 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-1791         TCGA-19-2619         TCGA-19-2620 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-2625         TCGA-19-2631         TCGA-19-5947 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-5950         TCGA-19-5951         TCGA-19-5952 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-5953         TCGA-19-5954         TCGA-19-5955 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-5956         TCGA-19-5958         TCGA-19-5959 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1440         TCGA-26-1442 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-26-6173         TCGA-26-6174         TCGA-27-1830 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1833 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1836         TCGA-27-2518 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-2528         TCGA-28-1746         TCGA-28-1747 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-1750         TCGA-28-1752         TCGA-28-1753 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-1757         TCGA-28-2501         TCGA-28-5208 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-5214         TCGA-32-1970         TCGA-32-1976 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-1978         TCGA-32-1982         TCGA-32-1986 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-1987         TCGA-32-1991         TCGA-32-4210 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-4211         TCGA-32-5222         TCGA-41-2573 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-41-2575         TCGA-41-3392         TCGA-41-3393 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-41-3915         TCGA-41-4097         TCGA-41-5651 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-41-6646         TCGA-74-6573         TCGA-74-6575 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-74-6577         TCGA-74-6578         TCGA-74-6581 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-74-6584         TCGA-76-4926         TCGA-76-4928 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931         TCGA-76-6192 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6193         TCGA-76-6282         TCGA-76-6283 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6285         TCGA-76-6656         TCGA-76-6657 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6660         TCGA-76-6662         TCGA-76-6663 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6664         TCGA-81-5910 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
D26V9, multiclass
[1] "Remove cluster labels:" "15Q GAIN CNV"          
clus
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2569         TCGA-06-2570 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0386         TCGA-12-0616         TCGA-12-0618 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-0619         TCGA-12-0821         TCGA-12-3650 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-5299         TCGA-14-0781         TCGA-14-0787 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-14-0789         TCGA-14-0790         TCGA-14-0817 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-14-1034         TCGA-14-1825         TCGA-14-1829 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-14-2554         TCGA-15-0742         TCGA-15-1444 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-16-0846         TCGA-16-1045         TCGA-19-1390 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2620 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-2624         TCGA-19-2625         TCGA-19-2629 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-4065         TCGA-19-5960         TCGA-26-1442 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-26-5135         TCGA-26-5136         TCGA-26-5139 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-1830         TCGA-27-1831         TCGA-27-1832 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1835         TCGA-27-1837 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-2519         TCGA-27-2521         TCGA-27-2523 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-2524         TCGA-27-2526         TCGA-27-2528 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-1747         TCGA-28-1753         TCGA-28-2509 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-2510         TCGA-28-2513         TCGA-28-2514 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5213         TCGA-28-5215 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-5216         TCGA-28-5220         TCGA-32-1970 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-4931 
"15Q GAIN WILD-TYPE" 
D26V10, multiclass
[1] "Remove cluster labels:" "15Q GAIN CNV"          
clus
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2569         TCGA-06-2570 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0386         TCGA-12-0616         TCGA-12-0618 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-0619         TCGA-12-0821         TCGA-12-3650 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-5299         TCGA-14-0781         TCGA-14-0787 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-14-0789         TCGA-14-0790         TCGA-14-0817 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-14-1034         TCGA-14-1825         TCGA-14-1829 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-14-2554         TCGA-15-0742         TCGA-15-1444 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-16-0846         TCGA-16-1045         TCGA-19-1390 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2620 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-2624         TCGA-19-2625         TCGA-19-2629 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-4065         TCGA-19-5960         TCGA-26-1442 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-26-5135         TCGA-26-5136         TCGA-26-5139 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-1830         TCGA-27-1831         TCGA-27-1832 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1835         TCGA-27-1837 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-2519         TCGA-27-2521         TCGA-27-2523 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-2524         TCGA-27-2526         TCGA-27-2528 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-1747         TCGA-28-1753         TCGA-28-2509 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-2510         TCGA-28-2513         TCGA-28-2514 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5213         TCGA-28-5215 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-5216         TCGA-28-5220         TCGA-32-1970 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-4931 
"15Q GAIN WILD-TYPE" 

Clustering(27) Variable = 16p gain
D27V1, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            3                144
  CLUS_2            6                 90
  CLUS_3            2                150
  CLUS_4            6                107
D27V2, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            3                114
  CLUS_2            9                162
  CLUS_3            5                215
D27V3, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            2                137
  CLUS_2            8                147
  CLUS_3            3                 70
  CLUS_4            4                100
D27V4, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            5                176
  CLUS_2            4                151
  CLUS_3            8                127
D27V5, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            9                152
  CLUS_2            6                182
  CLUS_3            2                210
D27V6, multiclass
D27V7, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            4                 50
  CLUS_2            2                 56
  CLUS_3            0                 44
  CLUS_4            1                 44
D27V8, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            1                 63
  CLUS_2            2                 31
  CLUS_3            4                100
D27V9, multiclass
[1] "Remove cluster labels:" "16P GAIN CNV"          
clus
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2559 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-2561         TCGA-06-2562         TCGA-06-2563 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-2564         TCGA-06-2565         TCGA-06-2569 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-2570         TCGA-06-5408         TCGA-06-5410 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-5411         TCGA-06-5412         TCGA-06-5413 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-5414         TCGA-06-5415         TCGA-06-5416 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-5418         TCGA-06-5856         TCGA-06-5858 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-5859         TCGA-08-0386         TCGA-12-0616 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-12-0618         TCGA-12-0619         TCGA-12-0821 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-12-3650         TCGA-12-3652         TCGA-12-3653 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5299         TCGA-14-0781 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-14-0787         TCGA-14-0789         TCGA-14-0790 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-14-0817         TCGA-14-1034         TCGA-14-1823 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-14-1825         TCGA-14-1829         TCGA-14-2554 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-15-0742         TCGA-15-1444         TCGA-16-0846 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-16-1045         TCGA-19-1390         TCGA-19-1787 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-19-2619         TCGA-19-2620         TCGA-19-2624 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-19-2625         TCGA-19-2629         TCGA-19-4065 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-26-5136         TCGA-26-5139         TCGA-27-1830 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1834 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-27-1835         TCGA-27-1837         TCGA-27-2519 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-27-2521         TCGA-27-2523         TCGA-27-2524 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-27-2526         TCGA-27-2528         TCGA-28-1747 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-28-1753         TCGA-28-2509         TCGA-28-2510 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-28-2513         TCGA-28-2514         TCGA-28-5204 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-28-5213         TCGA-28-5215         TCGA-28-5216 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-28-5218         TCGA-28-5220         TCGA-32-1970 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-76-4931 
"16P GAIN WILD-TYPE" 
D27V10, multiclass
[1] "Remove cluster labels:" "16P GAIN CNV"          
clus
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2559 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-2561         TCGA-06-2562         TCGA-06-2563 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-2564         TCGA-06-2565         TCGA-06-2569 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-2570         TCGA-06-5408         TCGA-06-5410 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-5411         TCGA-06-5412         TCGA-06-5413 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-5414         TCGA-06-5415         TCGA-06-5416 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-5418         TCGA-06-5856         TCGA-06-5858 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-5859         TCGA-08-0386         TCGA-12-0616 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-12-0618         TCGA-12-0619         TCGA-12-0821 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-12-3650         TCGA-12-3652         TCGA-12-3653 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5299         TCGA-14-0781 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-14-0787         TCGA-14-0789         TCGA-14-0790 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-14-0817         TCGA-14-1034         TCGA-14-1823 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-14-1825         TCGA-14-1829         TCGA-14-2554 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-15-0742         TCGA-15-1444         TCGA-16-0846 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-16-1045         TCGA-19-1390         TCGA-19-1787 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-19-2619         TCGA-19-2620         TCGA-19-2624 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-19-2625         TCGA-19-2629         TCGA-19-4065 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-26-5136         TCGA-26-5139         TCGA-27-1830 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1834 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-27-1835         TCGA-27-1837         TCGA-27-2519 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-27-2521         TCGA-27-2523         TCGA-27-2524 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-27-2526         TCGA-27-2528         TCGA-28-1747 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-28-1753         TCGA-28-2509         TCGA-28-2510 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-28-2513         TCGA-28-2514         TCGA-28-5204 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-28-5213         TCGA-28-5215         TCGA-28-5216 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-28-5218         TCGA-28-5220         TCGA-32-1970 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-76-4931 
"16P GAIN WILD-TYPE" 

Clustering(28) Variable = 16q gain
D28V1, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            2                145
  CLUS_2            7                 89
  CLUS_3            3                149
  CLUS_4            5                108
D28V2, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            4                113
  CLUS_2            9                162
  CLUS_3            4                216
D28V3, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            2                137
  CLUS_2            8                147
  CLUS_3            4                 69
  CLUS_4            3                101
D28V4, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            4                177
  CLUS_2            3                152
  CLUS_3           10                125
D28V5, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            9                152
  CLUS_2            6                182
  CLUS_3            2                210
D28V6, multiclass
D28V7, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            3                 51
  CLUS_2            3                 55
  CLUS_3            0                 44
  CLUS_4            1                 44
D28V8, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            1                 63
  CLUS_2            2                 31
  CLUS_3            4                100
D28V9, multiclass
[1] "Remove cluster labels:" "16Q GAIN CNV"          
clus
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2559 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-2561         TCGA-06-2562         TCGA-06-2563 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-2564         TCGA-06-2565         TCGA-06-2567 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-2569         TCGA-06-2570         TCGA-06-5408 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-5410         TCGA-06-5411         TCGA-06-5412 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-5413         TCGA-06-5414         TCGA-06-5415 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-5416         TCGA-06-5418         TCGA-06-5856 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-5858         TCGA-06-5859         TCGA-08-0386 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-12-0616         TCGA-12-0618         TCGA-12-0619 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-12-0821         TCGA-12-3650         TCGA-12-3652 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-12-3653         TCGA-12-5295         TCGA-12-5299 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-14-0781         TCGA-14-0787         TCGA-14-0789 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-14-0790         TCGA-14-0817         TCGA-14-1034 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-14-1823         TCGA-14-1825         TCGA-14-1829 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-14-2554         TCGA-15-0742         TCGA-15-1444 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-16-0846         TCGA-16-1045         TCGA-19-1390 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2624 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-19-2625         TCGA-19-2629         TCGA-19-4065 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-26-5136         TCGA-26-5139         TCGA-27-1830 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1834 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-27-1835         TCGA-27-1837         TCGA-27-2519 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-27-2521         TCGA-27-2523         TCGA-27-2524 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-27-2526         TCGA-27-2528         TCGA-28-1747 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-28-1753         TCGA-28-2509         TCGA-28-2510 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-28-2513         TCGA-28-2514         TCGA-28-5204 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-28-5213         TCGA-28-5215         TCGA-28-5216 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-28-5218         TCGA-28-5220         TCGA-32-1970 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-76-4931 
"16Q GAIN WILD-TYPE" 
D28V10, multiclass
[1] "Remove cluster labels:" "16Q GAIN CNV"          
clus
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2559 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-2561         TCGA-06-2562         TCGA-06-2563 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-2564         TCGA-06-2565         TCGA-06-2567 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-2569         TCGA-06-2570         TCGA-06-5408 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-5410         TCGA-06-5411         TCGA-06-5412 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-5413         TCGA-06-5414         TCGA-06-5415 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-5416         TCGA-06-5418         TCGA-06-5856 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-5858         TCGA-06-5859         TCGA-08-0386 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-12-0616         TCGA-12-0618         TCGA-12-0619 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-12-0821         TCGA-12-3650         TCGA-12-3652 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-12-3653         TCGA-12-5295         TCGA-12-5299 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-14-0781         TCGA-14-0787         TCGA-14-0789 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-14-0790         TCGA-14-0817         TCGA-14-1034 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-14-1823         TCGA-14-1825         TCGA-14-1829 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-14-2554         TCGA-15-0742         TCGA-15-1444 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-16-0846         TCGA-16-1045         TCGA-19-1390 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2624 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-19-2625         TCGA-19-2629         TCGA-19-4065 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-26-5136         TCGA-26-5139         TCGA-27-1830 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1834 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-27-1835         TCGA-27-1837         TCGA-27-2519 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-27-2521         TCGA-27-2523         TCGA-27-2524 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-27-2526         TCGA-27-2528         TCGA-28-1747 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-28-1753         TCGA-28-2509         TCGA-28-2510 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-28-2513         TCGA-28-2514         TCGA-28-5204 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-28-5213         TCGA-28-5215         TCGA-28-5216 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-28-5218         TCGA-28-5220         TCGA-32-1970 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-76-4931 
"16Q GAIN WILD-TYPE" 

Clustering(29) Variable = 17p gain
D29V1, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            2                145
  CLUS_2            3                 93
  CLUS_3            0                152
  CLUS_4            5                108
D29V2, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            1                116
  CLUS_2            5                166
  CLUS_3            4                216
D29V3, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            3                136
  CLUS_2            5                150
  CLUS_3            2                 71
  CLUS_4            1                103
D29V4, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            5                176
  CLUS_2            2                153
  CLUS_3            4                131
D29V5, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            6                155
  CLUS_2            1                187
  CLUS_3            4                208
D29V6, multiclass
[1] "Remove cluster labels:" "17P GAIN CNV"          
clus
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 2                107 
        TCGA-06-0650         TCGA-06-1804         TCGA-06-1806 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5299         TCGA-14-0740 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-14-0781         TCGA-14-0862         TCGA-14-1043 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-14-1395         TCGA-14-1450         TCGA-15-1444 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-19-4065         TCGA-19-5947         TCGA-19-5950 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-19-5951         TCGA-19-5952         TCGA-19-5953 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-19-5954         TCGA-19-5955         TCGA-19-5956 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-19-5958         TCGA-19-5959         TCGA-19-5960 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-26-1442         TCGA-26-5132         TCGA-26-5133 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-26-5134         TCGA-26-5135         TCGA-26-5136 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-26-5139         TCGA-26-6173         TCGA-26-6174 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-2501         TCGA-28-2510         TCGA-28-5204 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-5211         TCGA-28-5213         TCGA-28-5214 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-5215         TCGA-28-5216         TCGA-28-5219 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-5220         TCGA-28-6450         TCGA-32-1979 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-5222         TCGA-41-5651 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-41-6646         TCGA-74-6573         TCGA-74-6575 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-74-6577         TCGA-74-6578         TCGA-74-6581 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-74-6584         TCGA-76-4925         TCGA-76-4926 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-76-4928         TCGA-76-4929         TCGA-76-4931 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-76-4934         TCGA-76-4935         TCGA-76-6191 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-76-6192         TCGA-76-6193         TCGA-76-6280 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-76-6282         TCGA-76-6283         TCGA-76-6285 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-76-6286         TCGA-76-6656         TCGA-76-6657 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-76-6660         TCGA-76-6661         TCGA-76-6662 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-76-6663         TCGA-76-6664         TCGA-81-5910 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-81-5911         TCGA-87-5896 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D29V7, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            1                 53
  CLUS_2            1                 57
  CLUS_3            0                 44
  CLUS_4            1                 44
D29V8, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            0                 64
  CLUS_2            1                 32
  CLUS_3            2                102
D29V9, multiclass
[1] "Remove cluster labels:" "17P GAIN CNV"          
clus
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 1                146 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2569         TCGA-06-2570 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-08-0386         TCGA-12-0616         TCGA-12-0618 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-12-0619         TCGA-12-0821         TCGA-12-3650 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-12-5299         TCGA-14-0781         TCGA-14-0787 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-14-0789         TCGA-14-0790         TCGA-14-0817 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-14-1034         TCGA-14-1823         TCGA-14-1825 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-14-1829         TCGA-14-2554         TCGA-15-0742 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-15-1444         TCGA-16-0846         TCGA-16-1045 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-19-1390         TCGA-19-1787         TCGA-19-2619 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-19-2620         TCGA-19-2624         TCGA-19-2625 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-19-2629         TCGA-19-4065         TCGA-19-5960 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-26-1442         TCGA-26-5132         TCGA-26-5133 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-26-5134         TCGA-26-5135         TCGA-26-5136 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-26-5139         TCGA-27-1830         TCGA-27-1831 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-27-1832         TCGA-27-1834         TCGA-27-1835 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-27-1837         TCGA-27-2519         TCGA-27-2521 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-27-2523         TCGA-27-2524         TCGA-27-2526 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-27-2528         TCGA-28-1747         TCGA-28-1753 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-2509         TCGA-28-2510         TCGA-28-2513 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-2514         TCGA-28-5204         TCGA-28-5207 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-5208         TCGA-28-5209         TCGA-28-5213 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-5215         TCGA-28-5216         TCGA-28-5220 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-32-1970         TCGA-32-1980         TCGA-32-1982 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-32-2615         TCGA-32-2616         TCGA-32-2632 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-32-2634         TCGA-32-2638         TCGA-32-4213 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-32-5222         TCGA-41-2571         TCGA-41-2572 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-41-3915         TCGA-41-4097         TCGA-41-5651 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-76-4925         TCGA-76-4926         TCGA-76-4928 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D29V10, multiclass
[1] "Remove cluster labels:" "17P GAIN CNV"          
clus
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 1                146 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2569         TCGA-06-2570 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-08-0386         TCGA-12-0616         TCGA-12-0618 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-12-0619         TCGA-12-0821         TCGA-12-3650 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-12-5299         TCGA-14-0781         TCGA-14-0787 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-14-0789         TCGA-14-0790         TCGA-14-0817 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-14-1034         TCGA-14-1823         TCGA-14-1825 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-14-1829         TCGA-14-2554         TCGA-15-0742 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-15-1444         TCGA-16-0846         TCGA-16-1045 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-19-1390         TCGA-19-1787         TCGA-19-2619 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-19-2620         TCGA-19-2624         TCGA-19-2625 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-19-2629         TCGA-19-4065         TCGA-19-5960 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-26-1442         TCGA-26-5132         TCGA-26-5133 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-26-5134         TCGA-26-5135         TCGA-26-5136 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-26-5139         TCGA-27-1830         TCGA-27-1831 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-27-1832         TCGA-27-1834         TCGA-27-1835 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-27-1837         TCGA-27-2519         TCGA-27-2521 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-27-2523         TCGA-27-2524         TCGA-27-2526 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-27-2528         TCGA-28-1747         TCGA-28-1753 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-2509         TCGA-28-2510         TCGA-28-2513 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-2514         TCGA-28-5204         TCGA-28-5207 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-5208         TCGA-28-5209         TCGA-28-5213 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-5215         TCGA-28-5216         TCGA-28-5220 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-32-1970         TCGA-32-1980         TCGA-32-1982 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-32-2615         TCGA-32-2616         TCGA-32-2632 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-32-2634         TCGA-32-2638         TCGA-32-4213 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-32-5222         TCGA-41-2571         TCGA-41-2572 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-41-3915         TCGA-41-4097         TCGA-41-5651 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-76-4925         TCGA-76-4926         TCGA-76-4928 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 

Clustering(30) Variable = 17q gain
D30V1, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            5                142
  CLUS_2            6                 90
  CLUS_3            3                149
  CLUS_4            4                109
D30V2, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            4                113
  CLUS_2            6                165
  CLUS_3            8                212
D30V3, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            5                134
  CLUS_2            7                148
  CLUS_3            3                 70
  CLUS_4            4                100
D30V4, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            7                174
  CLUS_2            4                151
  CLUS_3            8                127
D30V5, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           10                151
  CLUS_2            3                185
  CLUS_3            6                206
D30V6, multiclass
[1] "Remove cluster labels:" "17Q GAIN CNV"          
clus
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                 2                107 
        TCGA-06-0650         TCGA-06-1804         TCGA-06-1806 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5299         TCGA-14-0740 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-14-0781         TCGA-14-0862         TCGA-14-1043 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-14-1395         TCGA-14-1450         TCGA-15-1444 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-19-4065         TCGA-19-5947         TCGA-19-5950 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-19-5951         TCGA-19-5952         TCGA-19-5953 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-19-5954         TCGA-19-5955         TCGA-19-5956 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-19-5958         TCGA-19-5959         TCGA-19-5960 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-26-1442         TCGA-26-5132         TCGA-26-5133 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-26-5134         TCGA-26-5135         TCGA-26-5136 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-26-5139         TCGA-26-6173         TCGA-26-6174 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-28-2501         TCGA-28-2510         TCGA-28-5204 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-28-5211         TCGA-28-5213         TCGA-28-5214 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-28-5215         TCGA-28-5216         TCGA-28-5219 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-28-5220         TCGA-28-6450         TCGA-32-1979 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-5222         TCGA-41-5651 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-41-6646         TCGA-74-6573         TCGA-74-6575 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-74-6577         TCGA-74-6578         TCGA-74-6581 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-74-6584         TCGA-76-4925         TCGA-76-4926 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-76-4928         TCGA-76-4929         TCGA-76-4931 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-76-4934         TCGA-76-4935         TCGA-76-6191 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-76-6192         TCGA-76-6193         TCGA-76-6280 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-76-6282         TCGA-76-6283         TCGA-76-6285 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-76-6286         TCGA-76-6656         TCGA-76-6657 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-76-6660         TCGA-76-6661         TCGA-76-6662 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-76-6663         TCGA-76-6664         TCGA-81-5910 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-81-5911         TCGA-87-5896 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
D30V7, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            2                 52
  CLUS_2            1                 57
  CLUS_3            0                 44
  CLUS_4            1                 44
D30V8, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            0                 64
  CLUS_2            1                 32
  CLUS_3            3                101
D30V9, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            0                 44
  CLUS_2            4                 63
  CLUS_3            1                 35
D30V10, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            3                 63
  CLUS_2            1                 20
  CLUS_3            1                 59

Clustering(31) Variable = 18p gain
D31V1, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            5                142
  CLUS_2           10                 86
  CLUS_3            4                148
  CLUS_4            6                107
D31V2, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            2                115
  CLUS_2            9                162
  CLUS_3           14                206
D31V3, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            5                134
  CLUS_2            9                146
  CLUS_3            2                 71
  CLUS_4            8                 96
D31V4, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1           12                169
  CLUS_2            6                149
  CLUS_3            6                129
D31V5, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1           17                144
  CLUS_2            8                180
  CLUS_3            2                210
D31V6, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            4                 35
  CLUS_2            2                 25
  CLUS_3            0                 16
  CLUS_4            0                 27
D31V7, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            4                 50
  CLUS_2            3                 55
  CLUS_3            2                 42
  CLUS_4            6                 39
D31V8, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            3                 61
  CLUS_2            2                 31
  CLUS_3           10                 94
D31V9, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            2                 42
  CLUS_2            8                 59
  CLUS_3            0                 36
D31V10, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            7                 59
  CLUS_2            1                 20
  CLUS_3            2                 58

Clustering(32) Variable = 18q gain
D32V1, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            5                142
  CLUS_2           10                 86
  CLUS_3            3                149
  CLUS_4            9                104
D32V2, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            2                115
  CLUS_2           11                160
  CLUS_3           14                206
D32V3, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            5                134
  CLUS_2           10                145
  CLUS_3            2                 71
  CLUS_4            9                 95
D32V4, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1           12                169
  CLUS_2            6                149
  CLUS_3            8                127
D32V5, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1           18                143
  CLUS_2            9                179
  CLUS_3            2                210
D32V6, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            4                 35
  CLUS_2            2                 25
  CLUS_3            0                 16
  CLUS_4            0                 27
D32V7, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            4                 50
  CLUS_2            5                 53
  CLUS_3            2                 42
  CLUS_4            5                 40
D32V8, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            3                 61
  CLUS_2            2                 31
  CLUS_3           11                 93
D32V9, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            1                 43
  CLUS_2            8                 59
  CLUS_3            0                 36
D32V10, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            7                 59
  CLUS_2            1                 20
  CLUS_3            1                 59

Clustering(33) Variable = 19p gain
D33V1, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1           36                111
  CLUS_2           24                 72
  CLUS_3           82                 70
  CLUS_4           15                 98
D33V2, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1           60                 57
  CLUS_2           29                142
  CLUS_3           68                152
D33V3, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1           51                 88
  CLUS_2           50                105
  CLUS_3           17                 56
  CLUS_4           34                 70
D33V4, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1           75                106
  CLUS_2           47                108
  CLUS_3           30                105
D33V5, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1           26                135
  CLUS_2           29                159
  CLUS_3          121                 91
D33V6, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            9                 30
  CLUS_2           14                 13
  CLUS_3            4                 12
  CLUS_4            1                 26
D33V7, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1           15                 39
  CLUS_2           13                 45
  CLUS_3           22                 22
  CLUS_4           11                 34
D33V8, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1           35                 29
  CLUS_2            6                 27
  CLUS_3           20                 84
D33V9, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            7                 37
  CLUS_2           22                 45
  CLUS_3           12                 24
D33V10, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1           16                 50
  CLUS_2           12                  9
  CLUS_3           13                 47

Clustering(34) Variable = 19q gain
D34V1, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1           31                116
  CLUS_2           16                 80
  CLUS_3           77                 75
  CLUS_4           10                103
D34V2, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1           56                 61
  CLUS_2           16                155
  CLUS_3           62                158
D34V3, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1           47                 92
  CLUS_2           41                114
  CLUS_3           13                 60
  CLUS_4           31                 73
D34V4, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1           68                113
  CLUS_2           43                112
  CLUS_3           21                114
D34V5, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1           14                147
  CLUS_2           22                166
  CLUS_3          115                 97
D34V6, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            8                 31
  CLUS_2           10                 17
  CLUS_3            4                 12
  CLUS_4            1                 26
D34V7, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1           11                 43
  CLUS_2           11                 47
  CLUS_3           18                 26
  CLUS_4            9                 36
D34V8, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1           30                 34
  CLUS_2            4                 29
  CLUS_3           15                 89
D34V9, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            5                 39
  CLUS_2           22                 45
  CLUS_3           11                 25
D34V10, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1           16                 50
  CLUS_2           11                 10
  CLUS_3           11                 49

Clustering(35) Variable = 20p gain
D35V1, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           36                111
  CLUS_2           21                 75
  CLUS_3           79                 73
  CLUS_4           19                 94
D35V2, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           64                 53
  CLUS_2           26                145
  CLUS_3           65                155
D35V3, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           43                 96
  CLUS_2           50                105
  CLUS_3           16                 57
  CLUS_4           39                 65
D35V4, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           71                110
  CLUS_2           54                101
  CLUS_3           23                112
D35V5, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           42                119
  CLUS_2           37                151
  CLUS_3          101                111
D35V6, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           14                 25
  CLUS_2           11                 16
  CLUS_3            5                 11
  CLUS_4            3                 24
D35V7, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           14                 40
  CLUS_2           12                 46
  CLUS_3           19                 25
  CLUS_4           14                 31
D35V8, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           29                 35
  CLUS_2            5                 28
  CLUS_3           25                 79
D35V9, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           11                 33
  CLUS_2           19                 48
  CLUS_3            9                 27
D35V10, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           15                 51
  CLUS_2           13                  8
  CLUS_3           11                 49

Clustering(36) Variable = 20q gain
D36V1, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           35                112
  CLUS_2           23                 73
  CLUS_3           79                 73
  CLUS_4           17                 96
D36V2, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           63                 54
  CLUS_2           25                146
  CLUS_3           66                154
D36V3, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           44                 95
  CLUS_2           50                105
  CLUS_3           15                 58
  CLUS_4           38                 66
D36V4, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           72                109
  CLUS_2           53                102
  CLUS_3           22                113
D36V5, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           40                121
  CLUS_2           38                150
  CLUS_3          100                112
D36V6, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           14                 25
  CLUS_2           11                 16
  CLUS_3            6                 10
  CLUS_4            2                 25
D36V7, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           15                 39
  CLUS_2           11                 47
  CLUS_3           19                 25
  CLUS_4           15                 30
D36V8, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           30                 34
  CLUS_2            5                 28
  CLUS_3           25                 79
D36V9, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           10                 34
  CLUS_2           19                 48
  CLUS_3            9                 27
D36V10, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           15                 51
  CLUS_2           13                  8
  CLUS_3           10                 50

Clustering(37) Variable = 21q gain
D37V1, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           16                131
  CLUS_2            6                 90
  CLUS_3            5                147
  CLUS_4            4                109
D37V2, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            4                113
  CLUS_2            5                166
  CLUS_3           22                198
D37V3, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           13                126
  CLUS_2            7                148
  CLUS_3            1                 72
  CLUS_4           13                 91
D37V4, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           10                171
  CLUS_2           21                134
  CLUS_3            3                132
D37V5, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           12                149
  CLUS_2           16                172
  CLUS_3            7                205
D37V6, multiclass
[1] "Remove cluster labels:" "21Q GAIN CNV"          
clus
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 2                107 
        TCGA-06-0650         TCGA-06-1804         TCGA-06-5408 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-06-5410         TCGA-06-5411         TCGA-06-5412 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-06-5413         TCGA-06-5414         TCGA-06-5415 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-06-5416         TCGA-06-5418         TCGA-06-5856 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-06-5858         TCGA-06-5859         TCGA-06-6388 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-06-6389         TCGA-06-6390         TCGA-06-6391 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-06-6693         TCGA-06-6694         TCGA-06-6695 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-06-6697         TCGA-06-6698         TCGA-06-6699 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-06-6700         TCGA-06-6701         TCGA-12-5295 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-12-5299         TCGA-12-5301         TCGA-14-0740 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-14-0781         TCGA-14-0862         TCGA-14-1043 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-14-1395         TCGA-14-1450         TCGA-15-1444 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-19-4065         TCGA-19-5947         TCGA-19-5950 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-19-5951         TCGA-19-5952         TCGA-19-5953 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-19-5954         TCGA-19-5955         TCGA-19-5956 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-19-5958         TCGA-19-5959         TCGA-19-5960 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-26-1442         TCGA-26-5132         TCGA-26-5133 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-26-5134         TCGA-26-5135         TCGA-26-5136 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-26-5139         TCGA-26-6173         TCGA-26-6174 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-28-2501         TCGA-28-2510         TCGA-28-5204 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-28-5211         TCGA-28-5213         TCGA-28-5214 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-28-5215         TCGA-28-5216         TCGA-28-5219 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-28-5220         TCGA-28-6450         TCGA-32-1979 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-5222         TCGA-41-5651 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-41-6646         TCGA-74-6573         TCGA-74-6575 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-74-6577         TCGA-74-6578         TCGA-74-6581 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-74-6584         TCGA-76-4925         TCGA-76-4926 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-76-4928         TCGA-76-4929         TCGA-76-4931 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-76-4934         TCGA-76-4935         TCGA-76-6191 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-76-6192         TCGA-76-6193         TCGA-76-6280 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-76-6282         TCGA-76-6283         TCGA-76-6285 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-76-6286         TCGA-76-6656         TCGA-76-6657 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-76-6660         TCGA-76-6661         TCGA-76-6662 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-76-6663         TCGA-76-6664         TCGA-81-5910 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-81-5911         TCGA-87-5896 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D37V7, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            5                 49
  CLUS_2            2                 56
  CLUS_3            2                 42
  CLUS_4            1                 44
D37V8, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            3                 61
  CLUS_2            2                 31
  CLUS_3            5                 99
D37V9, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            0                 44
  CLUS_2            9                 58
  CLUS_3            2                 34
D37V10, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            9                 57
  CLUS_2            1                 20
  CLUS_3            1                 59

Clustering(38) Variable = 22q gain
D38V1, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            2                145
  CLUS_2            5                 91
  CLUS_3            0                152
  CLUS_4            3                110
D38V2, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            0                117
  CLUS_2            4                167
  CLUS_3            6                214
D38V3, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            1                138
  CLUS_2            2                153
  CLUS_3            2                 71
  CLUS_4            5                 99
D38V4, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            2                179
  CLUS_2            5                150
  CLUS_3            3                132
D38V5, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            6                155
  CLUS_2            4                184
  CLUS_3            1                211
D38V6, multiclass
[1] "Remove cluster labels:" "22Q GAIN CNV"          
clus
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 1                108 
        TCGA-06-0650         TCGA-06-1804         TCGA-06-1806 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5299         TCGA-12-5301 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-14-0740         TCGA-14-0781         TCGA-14-0862 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-14-1043         TCGA-14-1395         TCGA-14-1450 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-15-1444         TCGA-19-4065         TCGA-19-5947 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-19-5950         TCGA-19-5951         TCGA-19-5952 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-19-5953         TCGA-19-5954         TCGA-19-5955 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-19-5956         TCGA-19-5958         TCGA-19-5959 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-26-5136         TCGA-26-5139         TCGA-26-6173 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-26-6174         TCGA-28-2501         TCGA-28-2510 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5211         TCGA-28-5213 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-5214         TCGA-28-5215         TCGA-28-5216 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-5219         TCGA-28-5220         TCGA-28-6450 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-32-1979         TCGA-32-1980         TCGA-32-5222 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-41-5651         TCGA-41-6646         TCGA-74-6573 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-74-6575         TCGA-74-6577         TCGA-74-6578 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-74-6581         TCGA-74-6584         TCGA-76-4925 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-76-4931         TCGA-76-4934         TCGA-76-4935 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-76-6191         TCGA-76-6192         TCGA-76-6193 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-76-6280         TCGA-76-6282         TCGA-76-6283 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-76-6285         TCGA-76-6286         TCGA-76-6656 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-76-6657         TCGA-76-6660         TCGA-76-6661 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-76-6662         TCGA-76-6663         TCGA-76-6664 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-81-5910         TCGA-81-5911         TCGA-87-5896 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
D38V7, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            1                 53
  CLUS_2            1                 57
  CLUS_3            0                 44
  CLUS_4            1                 44
D38V8, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            0                 64
  CLUS_2            1                 32
  CLUS_3            2                102
D38V9, multiclass
[1] "Remove cluster labels:" "22Q GAIN CNV"          
clus
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2570         TCGA-06-5408 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-5410         TCGA-06-5411         TCGA-06-5412 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-5413         TCGA-06-5414         TCGA-06-5415 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-5416         TCGA-06-5418         TCGA-06-5856 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-5858         TCGA-06-5859         TCGA-08-0386 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-12-0616         TCGA-12-0618         TCGA-12-0619 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-12-0821         TCGA-12-3650         TCGA-12-3652 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-12-3653         TCGA-12-5295         TCGA-12-5299 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-14-0781         TCGA-14-0787         TCGA-14-0789 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-14-0790         TCGA-14-0817         TCGA-14-1034 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-14-1823         TCGA-14-1825         TCGA-14-1829 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-14-2554         TCGA-15-0742         TCGA-15-1444 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-16-0846         TCGA-16-1045         TCGA-19-1390 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2620 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-19-2624         TCGA-19-2625         TCGA-19-2629 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-19-4065         TCGA-19-5960         TCGA-26-1442 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-26-5135         TCGA-26-5136         TCGA-26-5139 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-27-1830         TCGA-27-1831         TCGA-27-1832 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1835         TCGA-27-1837 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-27-2519         TCGA-27-2521         TCGA-27-2523 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-27-2524         TCGA-27-2526         TCGA-27-2528 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-1747         TCGA-28-1753         TCGA-28-2509 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-2510         TCGA-28-2513         TCGA-28-2514 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5213         TCGA-28-5215 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-5216         TCGA-28-5220         TCGA-32-1970 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-76-4931 
"22Q GAIN WILD-TYPE" 
D38V10, multiclass
[1] "Remove cluster labels:" "22Q GAIN CNV"          
clus
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2570         TCGA-06-5408 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-5410         TCGA-06-5411         TCGA-06-5412 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-5413         TCGA-06-5414         TCGA-06-5415 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-5416         TCGA-06-5418         TCGA-06-5856 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-5858         TCGA-06-5859         TCGA-08-0386 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-12-0616         TCGA-12-0618         TCGA-12-0619 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-12-0821         TCGA-12-3650         TCGA-12-3652 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-12-3653         TCGA-12-5295         TCGA-12-5299 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-14-0781         TCGA-14-0787         TCGA-14-0789 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-14-0790         TCGA-14-0817         TCGA-14-1034 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-14-1823         TCGA-14-1825         TCGA-14-1829 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-14-2554         TCGA-15-0742         TCGA-15-1444 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-16-0846         TCGA-16-1045         TCGA-19-1390 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2620 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-19-2624         TCGA-19-2625         TCGA-19-2629 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-19-4065         TCGA-19-5960         TCGA-26-1442 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-26-5135         TCGA-26-5136         TCGA-26-5139 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-27-1830         TCGA-27-1831         TCGA-27-1832 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1835         TCGA-27-1837 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-27-2519         TCGA-27-2521         TCGA-27-2523 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-27-2524         TCGA-27-2526         TCGA-27-2528 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-1747         TCGA-28-1753         TCGA-28-2509 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-2510         TCGA-28-2513         TCGA-28-2514 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5213         TCGA-28-5215 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-5216         TCGA-28-5220         TCGA-32-1970 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-76-4931 
"22Q GAIN WILD-TYPE" 

Clustering(39) Variable = Xq gain
D39V1, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           1               146
  CLUS_2           1                95
  CLUS_3           0               152
  CLUS_4           1               112
D39V2, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           0               117
  CLUS_2           1               170
  CLUS_3           2               218
D39V3, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           0               139
  CLUS_2           2               153
  CLUS_3           1                72
  CLUS_4           0               104
D39V4, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           2               179
  CLUS_2           0               155
  CLUS_3           1               134
D39V5, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           2               159
  CLUS_2           1               187
  CLUS_3           0               212
D39V6, multiclass
D39V7, multiclass
[1] "Remove cluster labels:" "XQ GAIN CNV"           
clus
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                1               200 
       TCGA-02-0003        TCGA-02-0011        TCGA-02-0014        TCGA-02-0068 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-02-0069        TCGA-02-0116        TCGA-02-2470        TCGA-02-2485 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0125        TCGA-06-0126        TCGA-06-0128        TCGA-06-0129 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0130        TCGA-06-0154        TCGA-06-0155        TCGA-06-0171 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0189        TCGA-06-0238        TCGA-06-0644        TCGA-06-0650 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0875        TCGA-06-0876        TCGA-06-0877        TCGA-06-0878 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0879        TCGA-06-0882        TCGA-06-0939        TCGA-06-1084 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-1086        TCGA-06-1087        TCGA-06-1800        TCGA-06-1802 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-1804        TCGA-06-1805        TCGA-06-1806        TCGA-06-2557 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-2558        TCGA-06-2559        TCGA-06-2562        TCGA-06-2563 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-2564        TCGA-06-2565        TCGA-06-2566        TCGA-06-2567 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-2570        TCGA-06-5408        TCGA-06-5410        TCGA-06-5411 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-5412        TCGA-06-5413        TCGA-06-5414        TCGA-06-5415 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-5416        TCGA-06-5418        TCGA-06-5856        TCGA-06-5858 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-5859        TCGA-06-6388        TCGA-06-6389        TCGA-06-6390 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-6391        TCGA-06-6693        TCGA-06-6694        TCGA-06-6695 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-6697        TCGA-06-6698        TCGA-06-6699        TCGA-06-6700 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-6701        TCGA-08-0245        TCGA-08-0344        TCGA-08-0345 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-08-0346        TCGA-08-0347        TCGA-08-0348        TCGA-08-0349 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-08-0350        TCGA-08-0351        TCGA-08-0352        TCGA-08-0353 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-08-0354        TCGA-08-0355        TCGA-08-0356        TCGA-08-0357 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-08-0358        TCGA-08-0359        TCGA-08-0375        TCGA-08-0380 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-08-0386        TCGA-08-0389        TCGA-08-0390        TCGA-08-0392 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-12-0691        TCGA-12-0692        TCGA-12-1598        TCGA-12-1599 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-12-3646        TCGA-12-3649        TCGA-12-3650        TCGA-12-3651 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-12-3652        TCGA-12-3653        TCGA-12-5295        TCGA-12-5301 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-14-0813        TCGA-14-0862        TCGA-14-0871        TCGA-14-1823 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-15-1446        TCGA-15-1447        TCGA-15-1449        TCGA-16-0846 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-16-1460        TCGA-19-0957        TCGA-19-0962        TCGA-19-1386 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-1389        TCGA-19-1390        TCGA-19-1392        TCGA-19-1786 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-1789        TCGA-19-1791        TCGA-19-2619        TCGA-19-2620 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-2625        TCGA-19-2631        TCGA-19-5947        TCGA-19-5950 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-5951        TCGA-19-5952        TCGA-19-5953        TCGA-19-5954 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-5955        TCGA-19-5956        TCGA-19-5958        TCGA-19-5959 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-5960        TCGA-26-1440        TCGA-26-1442        TCGA-26-5132 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-26-5133        TCGA-26-5134        TCGA-26-6173        TCGA-26-6174 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-27-1830        TCGA-27-1831        TCGA-27-1832        TCGA-27-1833 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-27-1834        TCGA-27-1836        TCGA-27-2518        TCGA-27-2528 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-1746        TCGA-28-1747        TCGA-28-1750        TCGA-28-1752 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-1753        TCGA-28-1757        TCGA-28-2501        TCGA-28-5208 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-5214        TCGA-32-1970        TCGA-32-1976        TCGA-32-1978 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-32-1982        TCGA-32-1986        TCGA-32-1987        TCGA-32-1991 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-32-4211        TCGA-32-5222        TCGA-41-2573        TCGA-41-2575 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-41-3392        TCGA-41-3393        TCGA-41-3915        TCGA-41-4097 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-41-5651        TCGA-41-6646        TCGA-74-6573        TCGA-74-6575 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-74-6577        TCGA-74-6578        TCGA-74-6581        TCGA-74-6584 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-76-4926        TCGA-76-4928        TCGA-76-4929        TCGA-76-4931 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-76-6192        TCGA-76-6193        TCGA-76-6282        TCGA-76-6283 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-76-6285        TCGA-76-6656        TCGA-76-6657        TCGA-76-6660 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-76-6662        TCGA-76-6663        TCGA-76-6664        TCGA-81-5910 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D39V8, multiclass
[1] "Remove cluster labels:" "XQ GAIN CNV"           
clus
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                1               200 
       TCGA-02-0003        TCGA-02-0011        TCGA-02-0014        TCGA-02-0068 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-02-0069        TCGA-02-0116        TCGA-02-2470        TCGA-02-2485 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0125        TCGA-06-0126        TCGA-06-0128        TCGA-06-0129 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0130        TCGA-06-0154        TCGA-06-0155        TCGA-06-0171 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0189        TCGA-06-0238        TCGA-06-0644        TCGA-06-0650 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0875        TCGA-06-0876        TCGA-06-0877        TCGA-06-0878 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0879        TCGA-06-0882        TCGA-06-0939        TCGA-06-1084 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-1086        TCGA-06-1087        TCGA-06-1800        TCGA-06-1802 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-1804        TCGA-06-1805        TCGA-06-1806        TCGA-06-2557 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-2558        TCGA-06-2559        TCGA-06-2562        TCGA-06-2563 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-2564        TCGA-06-2565        TCGA-06-2566        TCGA-06-2567 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-2570        TCGA-06-5408        TCGA-06-5410        TCGA-06-5411 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-5412        TCGA-06-5413        TCGA-06-5414        TCGA-06-5415 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-5416        TCGA-06-5418        TCGA-06-5856        TCGA-06-5858 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-5859        TCGA-06-6388        TCGA-06-6389        TCGA-06-6390 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-6391        TCGA-06-6693        TCGA-06-6694        TCGA-06-6695 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-6697        TCGA-06-6698        TCGA-06-6699        TCGA-06-6700 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-6701        TCGA-08-0245        TCGA-08-0344        TCGA-08-0345 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-08-0346        TCGA-08-0347        TCGA-08-0348        TCGA-08-0349 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-08-0350        TCGA-08-0351        TCGA-08-0352        TCGA-08-0353 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-08-0354        TCGA-08-0355        TCGA-08-0356        TCGA-08-0357 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-08-0358        TCGA-08-0359        TCGA-08-0375        TCGA-08-0380 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-08-0386        TCGA-08-0389        TCGA-08-0390        TCGA-08-0392 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-12-0691        TCGA-12-0692        TCGA-12-1598        TCGA-12-1599 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-12-3646        TCGA-12-3649        TCGA-12-3650        TCGA-12-3651 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-12-3652        TCGA-12-3653        TCGA-12-5295        TCGA-12-5301 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-14-0813        TCGA-14-0862        TCGA-14-0871        TCGA-14-1823 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-15-1446        TCGA-15-1447        TCGA-15-1449        TCGA-16-0846 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-16-1460        TCGA-19-0957        TCGA-19-0962        TCGA-19-1386 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-1389        TCGA-19-1390        TCGA-19-1392        TCGA-19-1786 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-1789        TCGA-19-1791        TCGA-19-2619        TCGA-19-2620 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-2625        TCGA-19-2631        TCGA-19-5947        TCGA-19-5950 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-5951        TCGA-19-5952        TCGA-19-5953        TCGA-19-5954 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-5955        TCGA-19-5956        TCGA-19-5958        TCGA-19-5959 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-5960        TCGA-26-1440        TCGA-26-1442        TCGA-26-5132 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-26-5133        TCGA-26-5134        TCGA-26-6173        TCGA-26-6174 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-27-1830        TCGA-27-1831        TCGA-27-1832        TCGA-27-1833 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-27-1834        TCGA-27-1836        TCGA-27-2518        TCGA-27-2528 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-1746        TCGA-28-1747        TCGA-28-1750        TCGA-28-1752 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-1753        TCGA-28-1757        TCGA-28-2501        TCGA-28-5208 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-5214        TCGA-32-1970        TCGA-32-1976        TCGA-32-1978 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-32-1982        TCGA-32-1986        TCGA-32-1987        TCGA-32-1991 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-32-4211        TCGA-32-5222        TCGA-41-2573        TCGA-41-2575 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-41-3392        TCGA-41-3393        TCGA-41-3915        TCGA-41-4097 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-41-5651        TCGA-41-6646        TCGA-74-6573        TCGA-74-6575 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-74-6577        TCGA-74-6578        TCGA-74-6581        TCGA-74-6584 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-76-4926        TCGA-76-4928        TCGA-76-4929        TCGA-76-4931 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-76-6192        TCGA-76-6193        TCGA-76-6282        TCGA-76-6283 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-76-6285        TCGA-76-6656        TCGA-76-6657        TCGA-76-6660 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-76-6662        TCGA-76-6663        TCGA-76-6664        TCGA-81-5910 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D39V9, multiclass
[1] "Remove cluster labels:" "XQ GAIN CNV"           
clus
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                1               146 
       TCGA-02-0047        TCGA-02-0055        TCGA-02-2483        TCGA-02-2485 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-02-2486        TCGA-06-0125        TCGA-06-0129        TCGA-06-0130 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0132        TCGA-06-0138        TCGA-06-0141        TCGA-06-0157 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0158        TCGA-06-0168        TCGA-06-0174        TCGA-06-0178 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0184        TCGA-06-0187        TCGA-06-0190        TCGA-06-0210 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0211        TCGA-06-0219        TCGA-06-0238        TCGA-06-0644 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0645        TCGA-06-0646        TCGA-06-0649        TCGA-06-0686 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0743        TCGA-06-0744        TCGA-06-0745        TCGA-06-0747 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0749        TCGA-06-0750        TCGA-06-0878        TCGA-06-0882 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-1804        TCGA-06-2557        TCGA-06-2558        TCGA-06-2559 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-2561        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2567        TCGA-06-2569        TCGA-06-2570 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-5408        TCGA-06-5410        TCGA-06-5411        TCGA-06-5412 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-5413        TCGA-06-5414        TCGA-06-5415        TCGA-06-5416 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-5418        TCGA-06-5856        TCGA-06-5858        TCGA-06-5859 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-08-0386        TCGA-12-0616        TCGA-12-0618        TCGA-12-0619 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-12-0821        TCGA-12-3650        TCGA-12-3652        TCGA-12-3653 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-12-5295        TCGA-12-5299        TCGA-14-0781        TCGA-14-0787 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-14-0789        TCGA-14-0790        TCGA-14-0817        TCGA-14-1034 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-14-1823        TCGA-14-1825        TCGA-14-1829        TCGA-14-2554 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-15-0742        TCGA-15-1444        TCGA-16-0846        TCGA-16-1045 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-1390        TCGA-19-2619        TCGA-19-2620        TCGA-19-2624 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-2625        TCGA-19-2629        TCGA-19-4065        TCGA-19-5960 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-27-1830 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-27-1831        TCGA-27-1832        TCGA-27-1834        TCGA-27-1835 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-27-1837        TCGA-27-2519        TCGA-27-2521        TCGA-27-2523 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-27-2524        TCGA-27-2526        TCGA-27-2528        TCGA-28-1747 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-1753        TCGA-28-2509        TCGA-28-2510        TCGA-28-2513 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-2514        TCGA-28-5204        TCGA-28-5207        TCGA-28-5208 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-5209        TCGA-28-5213        TCGA-28-5215        TCGA-28-5216 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5220        TCGA-32-1970        TCGA-32-1980 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-32-1982        TCGA-32-2615        TCGA-32-2616        TCGA-32-2632 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-32-2634        TCGA-32-2638        TCGA-32-4213        TCGA-32-5222 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-41-2571        TCGA-41-2572        TCGA-41-3915        TCGA-41-4097 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-41-5651        TCGA-76-4925        TCGA-76-4926        TCGA-76-4928 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-76-4929        TCGA-76-4931 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D39V10, multiclass
[1] "Remove cluster labels:" "XQ GAIN CNV"           
clus
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                1               146 
       TCGA-02-0047        TCGA-02-0055        TCGA-02-2483        TCGA-02-2485 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-02-2486        TCGA-06-0125        TCGA-06-0129        TCGA-06-0130 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0132        TCGA-06-0138        TCGA-06-0141        TCGA-06-0157 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0158        TCGA-06-0168        TCGA-06-0174        TCGA-06-0178 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0184        TCGA-06-0187        TCGA-06-0190        TCGA-06-0210 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0211        TCGA-06-0219        TCGA-06-0238        TCGA-06-0644 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0645        TCGA-06-0646        TCGA-06-0649        TCGA-06-0686 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0743        TCGA-06-0744        TCGA-06-0745        TCGA-06-0747 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0749        TCGA-06-0750        TCGA-06-0878        TCGA-06-0882 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-1804        TCGA-06-2557        TCGA-06-2558        TCGA-06-2559 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-2561        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2567        TCGA-06-2569        TCGA-06-2570 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-5408        TCGA-06-5410        TCGA-06-5411        TCGA-06-5412 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-5413        TCGA-06-5414        TCGA-06-5415        TCGA-06-5416 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-5418        TCGA-06-5856        TCGA-06-5858        TCGA-06-5859 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-08-0386        TCGA-12-0616        TCGA-12-0618        TCGA-12-0619 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-12-0821        TCGA-12-3650        TCGA-12-3652        TCGA-12-3653 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-12-5295        TCGA-12-5299        TCGA-14-0781        TCGA-14-0787 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-14-0789        TCGA-14-0790        TCGA-14-0817        TCGA-14-1034 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-14-1823        TCGA-14-1825        TCGA-14-1829        TCGA-14-2554 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-15-0742        TCGA-15-1444        TCGA-16-0846        TCGA-16-1045 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-1390        TCGA-19-2619        TCGA-19-2620        TCGA-19-2624 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-2625        TCGA-19-2629        TCGA-19-4065        TCGA-19-5960 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-27-1830 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-27-1831        TCGA-27-1832        TCGA-27-1834        TCGA-27-1835 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-27-1837        TCGA-27-2519        TCGA-27-2521        TCGA-27-2523 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-27-2524        TCGA-27-2526        TCGA-27-2528        TCGA-28-1747 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-1753        TCGA-28-2509        TCGA-28-2510        TCGA-28-2513 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-2514        TCGA-28-5204        TCGA-28-5207        TCGA-28-5208 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-5209        TCGA-28-5213        TCGA-28-5215        TCGA-28-5216 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5220        TCGA-32-1970        TCGA-32-1980 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-32-1982        TCGA-32-2615        TCGA-32-2616        TCGA-32-2632 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-32-2634        TCGA-32-2638        TCGA-32-4213        TCGA-32-5222 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-41-2571        TCGA-41-2572        TCGA-41-3915        TCGA-41-4097 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-41-5651        TCGA-76-4925        TCGA-76-4926        TCGA-76-4928 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-76-4929        TCGA-76-4931 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 

Clustering(40) Variable = 1p loss
D40V1, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           1               146
  CLUS_2           2                94
  CLUS_3           1               151
  CLUS_4           0               113
D40V2, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           1               116
  CLUS_2           2               169
  CLUS_3           1               219
D40V3, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           1               138
  CLUS_2           2               153
  CLUS_3           0                73
  CLUS_4           1               103
D40V4, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           1               180
  CLUS_2           0               155
  CLUS_3           3               132
D40V5, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           1               160
  CLUS_2           3               185
  CLUS_3           1               211
D40V6, multiclass
[1] "Remove cluster labels:" "1P LOSS CNV"           
clus
      1P LOSS CNV 1P LOSS WILD-TYPE 
                1               108 
       TCGA-06-0650        TCGA-06-1804        TCGA-06-1806        TCGA-06-5408 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-06-6388 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-6389        TCGA-06-6390        TCGA-06-6391        TCGA-06-6693 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-6694        TCGA-06-6695        TCGA-06-6697        TCGA-06-6698 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-6699        TCGA-06-6700        TCGA-06-6701        TCGA-12-5295 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-12-5299        TCGA-12-5301        TCGA-14-0781        TCGA-14-0862 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-14-1043        TCGA-14-1395        TCGA-14-1450        TCGA-15-1444 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-4065        TCGA-19-5947        TCGA-19-5950        TCGA-19-5951 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-5952        TCGA-19-5953        TCGA-19-5954        TCGA-19-5955 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-5956        TCGA-19-5958        TCGA-19-5959        TCGA-19-5960 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-26-6173 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-26-6174        TCGA-28-2501        TCGA-28-2510        TCGA-28-5204 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-5207        TCGA-28-5208        TCGA-28-5209        TCGA-28-5211 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-5213        TCGA-28-5214        TCGA-28-5215        TCGA-28-5216 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5219        TCGA-28-5220        TCGA-28-6450 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-32-1979        TCGA-32-1980        TCGA-32-5222        TCGA-41-5651 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4925 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-4926        TCGA-76-4928        TCGA-76-4929        TCGA-76-4931 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-4934        TCGA-76-4935        TCGA-76-6191        TCGA-76-6192 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-6193        TCGA-76-6280        TCGA-76-6282        TCGA-76-6283 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-6285        TCGA-76-6286        TCGA-76-6656        TCGA-76-6657 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-6660        TCGA-76-6661        TCGA-76-6662        TCGA-76-6663 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-6664        TCGA-81-5910        TCGA-81-5911        TCGA-87-5896 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D40V7, multiclass
[1] "Remove cluster labels:" "1P LOSS CNV"           
clus
      1P LOSS CNV 1P LOSS WILD-TYPE 
                2               199 
       TCGA-02-0003        TCGA-02-0011        TCGA-02-0014        TCGA-02-0068 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-02-0069        TCGA-02-0116        TCGA-02-2470        TCGA-02-2485 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0125        TCGA-06-0126        TCGA-06-0128        TCGA-06-0129 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0130        TCGA-06-0154        TCGA-06-0155        TCGA-06-0171 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0189        TCGA-06-0238        TCGA-06-0644        TCGA-06-0650 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0875        TCGA-06-0876        TCGA-06-0877        TCGA-06-0878 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0879        TCGA-06-0882        TCGA-06-0939        TCGA-06-1084 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-1086        TCGA-06-1087        TCGA-06-1800        TCGA-06-1802 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-1804        TCGA-06-1805        TCGA-06-1806        TCGA-06-2557 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-2558        TCGA-06-2559        TCGA-06-2562        TCGA-06-2563 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-2564        TCGA-06-2565        TCGA-06-2566        TCGA-06-2567 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-2570        TCGA-06-5408        TCGA-06-5410        TCGA-06-5411 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5412        TCGA-06-5413        TCGA-06-5414        TCGA-06-5415 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5416        TCGA-06-5418        TCGA-06-5856        TCGA-06-5858 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5859        TCGA-06-6388        TCGA-06-6389        TCGA-06-6390 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-6391        TCGA-06-6693        TCGA-06-6694        TCGA-06-6695 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-6697        TCGA-06-6698        TCGA-06-6699        TCGA-06-6700 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-6701        TCGA-08-0245        TCGA-08-0345        TCGA-08-0346 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-08-0347        TCGA-08-0348        TCGA-08-0349        TCGA-08-0350 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-08-0351        TCGA-08-0352        TCGA-08-0353        TCGA-08-0354 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-08-0355        TCGA-08-0356        TCGA-08-0357        TCGA-08-0358 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-08-0359        TCGA-08-0375        TCGA-08-0380        TCGA-08-0386 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-08-0389        TCGA-08-0390        TCGA-08-0392        TCGA-12-0691 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-12-0692        TCGA-12-1598        TCGA-12-1599        TCGA-12-3646 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-12-3649        TCGA-12-3650        TCGA-12-3651        TCGA-12-3652 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-12-3653        TCGA-12-5295        TCGA-12-5301        TCGA-14-0813 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-14-0862        TCGA-14-0871        TCGA-14-1823        TCGA-15-1446 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-15-1447        TCGA-15-1449        TCGA-16-0846        TCGA-16-1460 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-0957        TCGA-19-0962        TCGA-19-1386        TCGA-19-1389 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-1392        TCGA-19-1786        TCGA-19-1789        TCGA-19-1791 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-2619        TCGA-19-2620        TCGA-19-2625        TCGA-19-2631 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-5947        TCGA-19-5950        TCGA-19-5951        TCGA-19-5952 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-5953        TCGA-19-5954        TCGA-19-5955        TCGA-19-5956 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-5958        TCGA-19-5959        TCGA-19-5960        TCGA-26-1440 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-26-6173        TCGA-26-6174        TCGA-27-1830        TCGA-27-1831 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-27-1832        TCGA-27-1833        TCGA-27-1834        TCGA-27-1836 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-27-2518        TCGA-27-2528        TCGA-28-1746        TCGA-28-1747 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-1750        TCGA-28-1752        TCGA-28-1753        TCGA-28-1757 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-2501        TCGA-28-5208        TCGA-28-5214        TCGA-32-1970 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-32-1976        TCGA-32-1978        TCGA-32-1982        TCGA-32-1986 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-32-1987        TCGA-32-1991        TCGA-32-4210        TCGA-32-4211 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-32-5222        TCGA-41-2573        TCGA-41-2575        TCGA-41-3392 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-41-3393        TCGA-41-3915        TCGA-41-4097        TCGA-41-5651 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4926 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-6192 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-6193        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-6656        TCGA-76-6657        TCGA-76-6660        TCGA-76-6662 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-6663        TCGA-76-6664        TCGA-81-5910 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D40V8, multiclass
[1] "Remove cluster labels:" "1P LOSS CNV"           
clus
      1P LOSS CNV 1P LOSS WILD-TYPE 
                2               199 
       TCGA-02-0003        TCGA-02-0011        TCGA-02-0014        TCGA-02-0068 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-02-0069        TCGA-02-0116        TCGA-02-2470        TCGA-02-2485 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0125        TCGA-06-0126        TCGA-06-0128        TCGA-06-0129 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0130        TCGA-06-0154        TCGA-06-0155        TCGA-06-0171 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0189        TCGA-06-0238        TCGA-06-0644        TCGA-06-0650 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0875        TCGA-06-0876        TCGA-06-0877        TCGA-06-0878 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0879        TCGA-06-0882        TCGA-06-0939        TCGA-06-1084 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-1086        TCGA-06-1087        TCGA-06-1800        TCGA-06-1802 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-1804        TCGA-06-1805        TCGA-06-1806        TCGA-06-2557 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-2558        TCGA-06-2559        TCGA-06-2562        TCGA-06-2563 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-2564        TCGA-06-2565        TCGA-06-2566        TCGA-06-2567 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-2570        TCGA-06-5408        TCGA-06-5410        TCGA-06-5411 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5412        TCGA-06-5413        TCGA-06-5414        TCGA-06-5415 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5416        TCGA-06-5418        TCGA-06-5856        TCGA-06-5858 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5859        TCGA-06-6388        TCGA-06-6389        TCGA-06-6390 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-6391        TCGA-06-6693        TCGA-06-6694        TCGA-06-6695 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-6697        TCGA-06-6698        TCGA-06-6699        TCGA-06-6700 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-6701        TCGA-08-0245        TCGA-08-0345        TCGA-08-0346 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-08-0347        TCGA-08-0348        TCGA-08-0349        TCGA-08-0350 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-08-0351        TCGA-08-0352        TCGA-08-0353        TCGA-08-0354 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-08-0355        TCGA-08-0356        TCGA-08-0357        TCGA-08-0358 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-08-0359        TCGA-08-0375        TCGA-08-0380        TCGA-08-0386 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-08-0389        TCGA-08-0390        TCGA-08-0392        TCGA-12-0691 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-12-0692        TCGA-12-1598        TCGA-12-1599        TCGA-12-3646 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-12-3649        TCGA-12-3650        TCGA-12-3651        TCGA-12-3652 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-12-3653        TCGA-12-5295        TCGA-12-5301        TCGA-14-0813 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-14-0862        TCGA-14-0871        TCGA-14-1823        TCGA-15-1446 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-15-1447        TCGA-15-1449        TCGA-16-0846        TCGA-16-1460 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-0957        TCGA-19-0962        TCGA-19-1386        TCGA-19-1389 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-1392        TCGA-19-1786        TCGA-19-1789        TCGA-19-1791 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-2619        TCGA-19-2620        TCGA-19-2625        TCGA-19-2631 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-5947        TCGA-19-5950        TCGA-19-5951        TCGA-19-5952 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-5953        TCGA-19-5954        TCGA-19-5955        TCGA-19-5956 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-5958        TCGA-19-5959        TCGA-19-5960        TCGA-26-1440 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-26-6173        TCGA-26-6174        TCGA-27-1830        TCGA-27-1831 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-27-1832        TCGA-27-1833        TCGA-27-1834        TCGA-27-1836 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-27-2518        TCGA-27-2528        TCGA-28-1746        TCGA-28-1747 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-1750        TCGA-28-1752        TCGA-28-1753        TCGA-28-1757 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-2501        TCGA-28-5208        TCGA-28-5214        TCGA-32-1970 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-32-1976        TCGA-32-1978        TCGA-32-1982        TCGA-32-1986 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-32-1987        TCGA-32-1991        TCGA-32-4210        TCGA-32-4211 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-32-5222        TCGA-41-2573        TCGA-41-2575        TCGA-41-3392 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-41-3393        TCGA-41-3915        TCGA-41-4097        TCGA-41-5651 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4926 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-6192 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-6193        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-6656        TCGA-76-6657        TCGA-76-6660        TCGA-76-6662 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-6663        TCGA-76-6664        TCGA-81-5910 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D40V9, multiclass
[1] "Remove cluster labels:" "1P LOSS CNV"           
clus
      1P LOSS CNV 1P LOSS WILD-TYPE 
                1               146 
       TCGA-02-0047        TCGA-02-0055        TCGA-02-2483        TCGA-02-2485 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-02-2486        TCGA-06-0125        TCGA-06-0129        TCGA-06-0130 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0132        TCGA-06-0138        TCGA-06-0141        TCGA-06-0157 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0158        TCGA-06-0168        TCGA-06-0174        TCGA-06-0178 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0184        TCGA-06-0187        TCGA-06-0190        TCGA-06-0210 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0211        TCGA-06-0219        TCGA-06-0238        TCGA-06-0644 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0645        TCGA-06-0646        TCGA-06-0649        TCGA-06-0686 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0743        TCGA-06-0744        TCGA-06-0745        TCGA-06-0747 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0749        TCGA-06-0750        TCGA-06-0878        TCGA-06-0882 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-1804        TCGA-06-2557        TCGA-06-2558        TCGA-06-2559 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-2561        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2567        TCGA-06-2569        TCGA-06-2570 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5408        TCGA-06-5410        TCGA-06-5411        TCGA-06-5412 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5413        TCGA-06-5414        TCGA-06-5415        TCGA-06-5416 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5418        TCGA-06-5856        TCGA-06-5858        TCGA-06-5859 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-08-0386        TCGA-12-0616        TCGA-12-0618        TCGA-12-0619 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-12-0821        TCGA-12-3650        TCGA-12-3652        TCGA-12-3653 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-12-5295        TCGA-12-5299        TCGA-14-0781        TCGA-14-0787 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-14-0789        TCGA-14-0790        TCGA-14-0817        TCGA-14-1034 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-14-1823        TCGA-14-1825        TCGA-14-1829        TCGA-14-2554 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-15-0742        TCGA-15-1444        TCGA-16-0846        TCGA-16-1045 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-1787        TCGA-19-2619        TCGA-19-2620        TCGA-19-2624 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-2625        TCGA-19-2629        TCGA-19-4065        TCGA-19-5960 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-27-1830 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-27-1831        TCGA-27-1832        TCGA-27-1834        TCGA-27-1835 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-27-1837        TCGA-27-2519        TCGA-27-2521        TCGA-27-2523 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-27-2524        TCGA-27-2526        TCGA-27-2528        TCGA-28-1747 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-1753        TCGA-28-2509        TCGA-28-2510        TCGA-28-2513 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-2514        TCGA-28-5204        TCGA-28-5207        TCGA-28-5208 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-5209        TCGA-28-5213        TCGA-28-5215        TCGA-28-5216 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5220        TCGA-32-1970        TCGA-32-1980 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-32-1982        TCGA-32-2615        TCGA-32-2616        TCGA-32-2632 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-32-2634        TCGA-32-2638        TCGA-32-4213        TCGA-32-5222 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-41-2571        TCGA-41-2572        TCGA-41-3915        TCGA-41-4097 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-41-5651        TCGA-76-4925        TCGA-76-4926        TCGA-76-4928 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-4929        TCGA-76-4931 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D40V10, multiclass
[1] "Remove cluster labels:" "1P LOSS CNV"           
clus
      1P LOSS CNV 1P LOSS WILD-TYPE 
                1               146 
       TCGA-02-0047        TCGA-02-0055        TCGA-02-2483        TCGA-02-2485 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-02-2486        TCGA-06-0125        TCGA-06-0129        TCGA-06-0130 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0132        TCGA-06-0138        TCGA-06-0141        TCGA-06-0157 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0158        TCGA-06-0168        TCGA-06-0174        TCGA-06-0178 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0184        TCGA-06-0187        TCGA-06-0190        TCGA-06-0210 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0211        TCGA-06-0219        TCGA-06-0238        TCGA-06-0644 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0645        TCGA-06-0646        TCGA-06-0649        TCGA-06-0686 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0743        TCGA-06-0744        TCGA-06-0745        TCGA-06-0747 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0749        TCGA-06-0750        TCGA-06-0878        TCGA-06-0882 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-1804        TCGA-06-2557        TCGA-06-2558        TCGA-06-2559 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-2561        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2567        TCGA-06-2569        TCGA-06-2570 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5408        TCGA-06-5410        TCGA-06-5411        TCGA-06-5412 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5413        TCGA-06-5414        TCGA-06-5415        TCGA-06-5416 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5418        TCGA-06-5856        TCGA-06-5858        TCGA-06-5859 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-08-0386        TCGA-12-0616        TCGA-12-0618        TCGA-12-0619 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-12-0821        TCGA-12-3650        TCGA-12-3652        TCGA-12-3653 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-12-5295        TCGA-12-5299        TCGA-14-0781        TCGA-14-0787 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-14-0789        TCGA-14-0790        TCGA-14-0817        TCGA-14-1034 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-14-1823        TCGA-14-1825        TCGA-14-1829        TCGA-14-2554 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-15-0742        TCGA-15-1444        TCGA-16-0846        TCGA-16-1045 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-1787        TCGA-19-2619        TCGA-19-2620        TCGA-19-2624 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-2625        TCGA-19-2629        TCGA-19-4065        TCGA-19-5960 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-27-1830 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-27-1831        TCGA-27-1832        TCGA-27-1834        TCGA-27-1835 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-27-1837        TCGA-27-2519        TCGA-27-2521        TCGA-27-2523 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-27-2524        TCGA-27-2526        TCGA-27-2528        TCGA-28-1747 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-1753        TCGA-28-2509        TCGA-28-2510        TCGA-28-2513 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-2514        TCGA-28-5204        TCGA-28-5207        TCGA-28-5208 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-5209        TCGA-28-5213        TCGA-28-5215        TCGA-28-5216 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5220        TCGA-32-1970        TCGA-32-1980 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-32-1982        TCGA-32-2615        TCGA-32-2616        TCGA-32-2632 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-32-2634        TCGA-32-2638        TCGA-32-4213        TCGA-32-5222 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-41-2571        TCGA-41-2572        TCGA-41-3915        TCGA-41-4097 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-41-5651        TCGA-76-4925        TCGA-76-4926        TCGA-76-4928 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-4929        TCGA-76-4931 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 

Clustering(41) Variable = 1q loss
D41V1, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0               147
  CLUS_2           1                95
  CLUS_3           2               150
  CLUS_4           0               113
D41V2, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           1               116
  CLUS_2           1               170
  CLUS_3           1               219
D41V3, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           2               137
  CLUS_2           1               154
  CLUS_3           0                73
  CLUS_4           0               104
D41V4, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           1               180
  CLUS_2           1               154
  CLUS_3           1               134
D41V5, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           1               160
  CLUS_2           1               187
  CLUS_3           2               210
D41V6, multiclass
[1] "Remove cluster labels:" "1Q LOSS CNV"           
clus
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                1               108 
       TCGA-06-0650        TCGA-06-1804        TCGA-06-1806        TCGA-06-5408 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-06-6388 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-6389        TCGA-06-6390        TCGA-06-6391        TCGA-06-6693 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-6694        TCGA-06-6695        TCGA-06-6697        TCGA-06-6698 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-6699        TCGA-06-6700        TCGA-06-6701        TCGA-12-5295 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-12-5299        TCGA-12-5301        TCGA-14-0781        TCGA-14-0862 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-14-1043        TCGA-14-1395        TCGA-14-1450        TCGA-15-1444 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-4065        TCGA-19-5947        TCGA-19-5950        TCGA-19-5951 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-5952        TCGA-19-5953        TCGA-19-5954        TCGA-19-5955 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-5956        TCGA-19-5958        TCGA-19-5959        TCGA-19-5960 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-26-6173 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-26-6174        TCGA-28-2501        TCGA-28-2510        TCGA-28-5204 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-5207        TCGA-28-5208        TCGA-28-5209        TCGA-28-5211 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-5213        TCGA-28-5214        TCGA-28-5215        TCGA-28-5216 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5219        TCGA-28-5220        TCGA-28-6450 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-32-1979        TCGA-32-1980        TCGA-32-5222        TCGA-41-5651 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4925 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-4926        TCGA-76-4928        TCGA-76-4929        TCGA-76-4931 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-4934        TCGA-76-4935        TCGA-76-6191        TCGA-76-6192 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-6193        TCGA-76-6280        TCGA-76-6282        TCGA-76-6283 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-6285        TCGA-76-6286        TCGA-76-6656        TCGA-76-6657 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-6660        TCGA-76-6661        TCGA-76-6662        TCGA-76-6663 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-6664        TCGA-81-5910        TCGA-81-5911        TCGA-87-5896 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
D41V7, multiclass
[1] "Remove cluster labels:" "1Q LOSS CNV"           
clus
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                1               200 
       TCGA-02-0003        TCGA-02-0011        TCGA-02-0014        TCGA-02-0068 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-02-0069        TCGA-02-0116        TCGA-02-2470        TCGA-02-2485 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0125        TCGA-06-0126        TCGA-06-0128        TCGA-06-0129 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0130        TCGA-06-0154        TCGA-06-0155        TCGA-06-0171 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0189        TCGA-06-0238        TCGA-06-0644        TCGA-06-0650 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0875        TCGA-06-0876        TCGA-06-0877        TCGA-06-0878 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0879        TCGA-06-0882        TCGA-06-0939        TCGA-06-1084 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-1086        TCGA-06-1087        TCGA-06-1800        TCGA-06-1802 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-1804        TCGA-06-1805        TCGA-06-1806        TCGA-06-2557 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-2558        TCGA-06-2559        TCGA-06-2562        TCGA-06-2563 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-2564        TCGA-06-2565        TCGA-06-2566        TCGA-06-2567 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-2570        TCGA-06-5408        TCGA-06-5410        TCGA-06-5411 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5412        TCGA-06-5413        TCGA-06-5414        TCGA-06-5415 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5416        TCGA-06-5418        TCGA-06-5856        TCGA-06-5858 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5859        TCGA-06-6388        TCGA-06-6389        TCGA-06-6390 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-6391        TCGA-06-6693        TCGA-06-6694        TCGA-06-6695 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-6697        TCGA-06-6698        TCGA-06-6699        TCGA-06-6700 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-6701        TCGA-08-0245        TCGA-08-0344        TCGA-08-0345 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-08-0346        TCGA-08-0347        TCGA-08-0348        TCGA-08-0349 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-08-0350        TCGA-08-0351        TCGA-08-0352        TCGA-08-0353 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-08-0354        TCGA-08-0355        TCGA-08-0356        TCGA-08-0357 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-08-0358        TCGA-08-0359        TCGA-08-0375        TCGA-08-0380 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-08-0386        TCGA-08-0389        TCGA-08-0390        TCGA-08-0392 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-12-0691        TCGA-12-0692        TCGA-12-1598        TCGA-12-1599 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-12-3646        TCGA-12-3649        TCGA-12-3650        TCGA-12-3651 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-12-3652        TCGA-12-3653        TCGA-12-5295        TCGA-12-5301 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-14-0813        TCGA-14-0862        TCGA-14-0871        TCGA-14-1823 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-15-1446        TCGA-15-1447        TCGA-15-1449        TCGA-16-0846 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-16-1460        TCGA-19-0957        TCGA-19-0962        TCGA-19-1386 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-1389        TCGA-19-1392        TCGA-19-1786        TCGA-19-1789 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-1791        TCGA-19-2619        TCGA-19-2620        TCGA-19-2625 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-2631        TCGA-19-5947        TCGA-19-5950        TCGA-19-5951 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-5952        TCGA-19-5953        TCGA-19-5954        TCGA-19-5955 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-5956        TCGA-19-5958        TCGA-19-5959        TCGA-19-5960 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-26-1440        TCGA-26-1442        TCGA-26-5132        TCGA-26-5133 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-26-5134        TCGA-26-6173        TCGA-26-6174        TCGA-27-1830 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-27-1831        TCGA-27-1832        TCGA-27-1833        TCGA-27-1834 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-27-1836        TCGA-27-2518        TCGA-27-2528        TCGA-28-1746 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-1747        TCGA-28-1750        TCGA-28-1752        TCGA-28-1753 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-1757        TCGA-28-2501        TCGA-28-5208        TCGA-28-5214 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-32-1970        TCGA-32-1976        TCGA-32-1978        TCGA-32-1982 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-32-1986        TCGA-32-1987        TCGA-32-1991        TCGA-32-4210 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-32-4211        TCGA-32-5222        TCGA-41-2573        TCGA-41-2575 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-41-3392        TCGA-41-3393        TCGA-41-3915        TCGA-41-4097 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-41-5651        TCGA-41-6646        TCGA-74-6573        TCGA-74-6575 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-74-6577        TCGA-74-6578        TCGA-74-6581        TCGA-74-6584 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-4926        TCGA-76-4928        TCGA-76-4929        TCGA-76-4931 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-6192        TCGA-76-6193        TCGA-76-6282        TCGA-76-6283 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-6285        TCGA-76-6656        TCGA-76-6657        TCGA-76-6660 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-6662        TCGA-76-6663        TCGA-76-6664        TCGA-81-5910 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
D41V8, multiclass
[1] "Remove cluster labels:" "1Q LOSS CNV"           
clus
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                1               200 
       TCGA-02-0003        TCGA-02-0011        TCGA-02-0014        TCGA-02-0068 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-02-0069        TCGA-02-0116        TCGA-02-2470        TCGA-02-2485 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0125        TCGA-06-0126        TCGA-06-0128        TCGA-06-0129 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0130        TCGA-06-0154        TCGA-06-0155        TCGA-06-0171 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0189        TCGA-06-0238        TCGA-06-0644        TCGA-06-0650 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0875        TCGA-06-0876        TCGA-06-0877        TCGA-06-0878 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0879        TCGA-06-0882        TCGA-06-0939        TCGA-06-1084 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-1086        TCGA-06-1087        TCGA-06-1800        TCGA-06-1802 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-1804        TCGA-06-1805        TCGA-06-1806        TCGA-06-2557 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-2558        TCGA-06-2559        TCGA-06-2562        TCGA-06-2563 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-2564        TCGA-06-2565        TCGA-06-2566        TCGA-06-2567 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-2570        TCGA-06-5408        TCGA-06-5410        TCGA-06-5411 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5412        TCGA-06-5413        TCGA-06-5414        TCGA-06-5415 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5416        TCGA-06-5418        TCGA-06-5856        TCGA-06-5858 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5859        TCGA-06-6388        TCGA-06-6389        TCGA-06-6390 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-6391        TCGA-06-6693        TCGA-06-6694        TCGA-06-6695 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-6697        TCGA-06-6698        TCGA-06-6699        TCGA-06-6700 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-6701        TCGA-08-0245        TCGA-08-0344        TCGA-08-0345 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-08-0346        TCGA-08-0347        TCGA-08-0348        TCGA-08-0349 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-08-0350        TCGA-08-0351        TCGA-08-0352        TCGA-08-0353 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-08-0354        TCGA-08-0355        TCGA-08-0356        TCGA-08-0357 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-08-0358        TCGA-08-0359        TCGA-08-0375        TCGA-08-0380 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-08-0386        TCGA-08-0389        TCGA-08-0390        TCGA-08-0392 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-12-0691        TCGA-12-0692        TCGA-12-1598        TCGA-12-1599 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-12-3646        TCGA-12-3649        TCGA-12-3650        TCGA-12-3651 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-12-3652        TCGA-12-3653        TCGA-12-5295        TCGA-12-5301 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-14-0813        TCGA-14-0862        TCGA-14-0871        TCGA-14-1823 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-15-1446        TCGA-15-1447        TCGA-15-1449        TCGA-16-0846 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-16-1460        TCGA-19-0957        TCGA-19-0962        TCGA-19-1386 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-1389        TCGA-19-1392        TCGA-19-1786        TCGA-19-1789 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-1791        TCGA-19-2619        TCGA-19-2620        TCGA-19-2625 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-2631        TCGA-19-5947        TCGA-19-5950        TCGA-19-5951 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-5952        TCGA-19-5953        TCGA-19-5954        TCGA-19-5955 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-5956        TCGA-19-5958        TCGA-19-5959        TCGA-19-5960 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-26-1440        TCGA-26-1442        TCGA-26-5132        TCGA-26-5133 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-26-5134        TCGA-26-6173        TCGA-26-6174        TCGA-27-1830 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-27-1831        TCGA-27-1832        TCGA-27-1833        TCGA-27-1834 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-27-1836        TCGA-27-2518        TCGA-27-2528        TCGA-28-1746 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-1747        TCGA-28-1750        TCGA-28-1752        TCGA-28-1753 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-1757        TCGA-28-2501        TCGA-28-5208        TCGA-28-5214 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-32-1970        TCGA-32-1976        TCGA-32-1978        TCGA-32-1982 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-32-1986        TCGA-32-1987        TCGA-32-1991        TCGA-32-4210 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-32-4211        TCGA-32-5222        TCGA-41-2573        TCGA-41-2575 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-41-3392        TCGA-41-3393        TCGA-41-3915        TCGA-41-4097 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-41-5651        TCGA-41-6646        TCGA-74-6573        TCGA-74-6575 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-74-6577        TCGA-74-6578        TCGA-74-6581        TCGA-74-6584 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-4926        TCGA-76-4928        TCGA-76-4929        TCGA-76-4931 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-6192        TCGA-76-6193        TCGA-76-6282        TCGA-76-6283 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-6285        TCGA-76-6656        TCGA-76-6657        TCGA-76-6660 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-6662        TCGA-76-6663        TCGA-76-6664        TCGA-81-5910 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
D41V9, multiclass
[1] "Remove cluster labels:" "1Q LOSS CNV"           
clus
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                2               145 
       TCGA-02-0047        TCGA-02-0055        TCGA-02-2483        TCGA-02-2485 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-02-2486        TCGA-06-0125        TCGA-06-0129        TCGA-06-0130 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0132        TCGA-06-0138        TCGA-06-0141        TCGA-06-0157 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0158        TCGA-06-0168        TCGA-06-0174        TCGA-06-0178 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0184        TCGA-06-0187        TCGA-06-0190        TCGA-06-0210 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0211        TCGA-06-0219        TCGA-06-0238        TCGA-06-0644 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0645        TCGA-06-0646        TCGA-06-0649        TCGA-06-0686 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0743        TCGA-06-0744        TCGA-06-0745        TCGA-06-0747 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0749        TCGA-06-0750        TCGA-06-0878        TCGA-06-0882 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-1804        TCGA-06-2557        TCGA-06-2558        TCGA-06-2559 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-2561        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2567        TCGA-06-2569        TCGA-06-2570 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5408        TCGA-06-5410        TCGA-06-5411        TCGA-06-5412 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5413        TCGA-06-5414        TCGA-06-5415        TCGA-06-5416 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5418        TCGA-06-5856        TCGA-06-5858        TCGA-06-5859 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-08-0386        TCGA-12-0616        TCGA-12-0618        TCGA-12-0619 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-12-0821        TCGA-12-3650        TCGA-12-3652        TCGA-12-3653 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-12-5295        TCGA-12-5299        TCGA-14-0781        TCGA-14-0787 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-14-0789        TCGA-14-0790        TCGA-14-0817        TCGA-14-1823 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-14-1825        TCGA-14-1829        TCGA-14-2554        TCGA-15-0742 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-15-1444        TCGA-16-0846        TCGA-16-1045        TCGA-19-1787 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-2619        TCGA-19-2620        TCGA-19-2624        TCGA-19-2625 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-2629        TCGA-19-4065        TCGA-19-5960        TCGA-26-1442 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-26-5132        TCGA-26-5133        TCGA-26-5134        TCGA-26-5135 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-26-5136        TCGA-26-5139        TCGA-27-1830        TCGA-27-1831 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-27-1832        TCGA-27-1834        TCGA-27-1835        TCGA-27-1837 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-27-2519        TCGA-27-2521        TCGA-27-2523        TCGA-27-2524 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-27-2526        TCGA-27-2528        TCGA-28-1747        TCGA-28-1753 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-2509        TCGA-28-2510        TCGA-28-2513        TCGA-28-2514 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-5204        TCGA-28-5207        TCGA-28-5208        TCGA-28-5209 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-5213        TCGA-28-5215        TCGA-28-5216        TCGA-28-5218 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-5220        TCGA-32-1970        TCGA-32-1980        TCGA-32-1982 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-32-2615        TCGA-32-2616        TCGA-32-2632        TCGA-32-2634 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-32-2638        TCGA-32-4213        TCGA-32-5222        TCGA-41-2571 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-41-2572        TCGA-41-3915        TCGA-41-4097        TCGA-41-5651 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-4925        TCGA-76-4926        TCGA-76-4928        TCGA-76-4929 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-4931 
"1Q LOSS WILD-TYPE" 
D41V10, multiclass
[1] "Remove cluster labels:" "1Q LOSS CNV"           
clus
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                2               145 
       TCGA-02-0047        TCGA-02-0055        TCGA-02-2483        TCGA-02-2485 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-02-2486        TCGA-06-0125        TCGA-06-0129        TCGA-06-0130 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0132        TCGA-06-0138        TCGA-06-0141        TCGA-06-0157 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0158        TCGA-06-0168        TCGA-06-0174        TCGA-06-0178 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0184        TCGA-06-0187        TCGA-06-0190        TCGA-06-0210 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0211        TCGA-06-0219        TCGA-06-0238        TCGA-06-0644 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0645        TCGA-06-0646        TCGA-06-0649        TCGA-06-0686 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0743        TCGA-06-0744        TCGA-06-0745        TCGA-06-0747 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0749        TCGA-06-0750        TCGA-06-0878        TCGA-06-0882 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-1804        TCGA-06-2557        TCGA-06-2558        TCGA-06-2559 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-2561        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2567        TCGA-06-2569        TCGA-06-2570 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5408        TCGA-06-5410        TCGA-06-5411        TCGA-06-5412 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5413        TCGA-06-5414        TCGA-06-5415        TCGA-06-5416 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5418        TCGA-06-5856        TCGA-06-5858        TCGA-06-5859 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-08-0386        TCGA-12-0616        TCGA-12-0618        TCGA-12-0619 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-12-0821        TCGA-12-3650        TCGA-12-3652        TCGA-12-3653 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-12-5295        TCGA-12-5299        TCGA-14-0781        TCGA-14-0787 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-14-0789        TCGA-14-0790        TCGA-14-0817        TCGA-14-1823 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-14-1825        TCGA-14-1829        TCGA-14-2554        TCGA-15-0742 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-15-1444        TCGA-16-0846        TCGA-16-1045        TCGA-19-1787 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-2619        TCGA-19-2620        TCGA-19-2624        TCGA-19-2625 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-2629        TCGA-19-4065        TCGA-19-5960        TCGA-26-1442 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-26-5132        TCGA-26-5133        TCGA-26-5134        TCGA-26-5135 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-26-5136        TCGA-26-5139        TCGA-27-1830        TCGA-27-1831 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-27-1832        TCGA-27-1834        TCGA-27-1835        TCGA-27-1837 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-27-2519        TCGA-27-2521        TCGA-27-2523        TCGA-27-2524 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-27-2526        TCGA-27-2528        TCGA-28-1747        TCGA-28-1753 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-2509        TCGA-28-2510        TCGA-28-2513        TCGA-28-2514 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-5204        TCGA-28-5207        TCGA-28-5208        TCGA-28-5209 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-5213        TCGA-28-5215        TCGA-28-5216        TCGA-28-5218 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-5220        TCGA-32-1970        TCGA-32-1980        TCGA-32-1982 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-32-2615        TCGA-32-2616        TCGA-32-2632        TCGA-32-2634 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-32-2638        TCGA-32-4213        TCGA-32-5222        TCGA-41-2571 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-41-2572        TCGA-41-3915        TCGA-41-4097        TCGA-41-5651 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-4925        TCGA-76-4926        TCGA-76-4928        TCGA-76-4929 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-4931 
"1Q LOSS WILD-TYPE" 

Clustering(42) Variable = 2p loss
D42V1, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           1               146
  CLUS_2           5                91
  CLUS_3           3               149
  CLUS_4           1               112
D42V2, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           2               115
  CLUS_2           7               164
  CLUS_3           1               219
D42V3, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           1               138
  CLUS_2           3               152
  CLUS_3           2                71
  CLUS_4           2               102
D42V4, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           1               180
  CLUS_2           1               154
  CLUS_3           6               129
D42V5, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           4               157
  CLUS_2           5               183
  CLUS_3           1               211
D42V6, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           0                39
  CLUS_2           1                26
  CLUS_3           0                16
  CLUS_4           2                25
D42V7, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           2                52
  CLUS_2           2                56
  CLUS_3           1                43
  CLUS_4           0                45
D42V8, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           1                63
  CLUS_2           1                32
  CLUS_3           3               101
D42V9, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           3                41
  CLUS_2           0                67
  CLUS_3           0                36
D42V10, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           0                66
  CLUS_2           0                21
  CLUS_3           3                57

Clustering(43) Variable = 2q loss
D43V1, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1               146
  CLUS_2           5                91
  CLUS_3           2               150
  CLUS_4           1               112
D43V2, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1               116
  CLUS_2           7               164
  CLUS_3           1               219
D43V3, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           0               139
  CLUS_2           3               152
  CLUS_3           2                71
  CLUS_4           2               102
D43V4, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           0               181
  CLUS_2           1               154
  CLUS_3           6               129
D43V5, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           3               158
  CLUS_2           5               183
  CLUS_3           1               211
D43V6, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           0                39
  CLUS_2           1                26
  CLUS_3           0                16
  CLUS_4           2                25
D43V7, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           2                52
  CLUS_2           2                56
  CLUS_3           1                43
  CLUS_4           0                45
D43V8, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1                63
  CLUS_2           1                32
  CLUS_3           3               101
D43V9, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           3                41
  CLUS_2           0                67
  CLUS_3           0                36
D43V10, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           0                66
  CLUS_2           0                21
  CLUS_3           3                57

Clustering(44) Variable = 3p loss
D44V1, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           6               141
  CLUS_2           3                93
  CLUS_3           6               146
  CLUS_4           6               107
D44V2, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           4               113
  CLUS_2           6               165
  CLUS_3          11               209
D44V3, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           5               134
  CLUS_2           5               150
  CLUS_3           5                68
  CLUS_4           5                99
D44V4, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           6               175
  CLUS_2           6               149
  CLUS_3           8               127
D44V5, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          10               151
  CLUS_2          10               178
  CLUS_3           2               210
D44V6, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           1                38
  CLUS_2           0                27
  CLUS_3           0                16
  CLUS_4           3                24
D44V7, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           2                52
  CLUS_2           0                58
  CLUS_3           4                40
  CLUS_4           3                42
D44V8, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           4                60
  CLUS_2           1                32
  CLUS_3           4               100
D44V9, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           3                41
  CLUS_2           3                64
  CLUS_3           0                36
D44V10, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           4                62
  CLUS_2           1                20
  CLUS_3           1                59

Clustering(45) Variable = 3q loss
D45V1, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           3               144
  CLUS_2           2                94
  CLUS_3           3               149
  CLUS_4           7               106
D45V2, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           2               115
  CLUS_2           4               167
  CLUS_3           9               211
D45V3, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           1               138
  CLUS_2           4               151
  CLUS_3           6                67
  CLUS_4           4               100
D45V4, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           6               175
  CLUS_2           3               152
  CLUS_3           6               129
D45V5, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1          10               151
  CLUS_2           6               182
  CLUS_3           0               212
D45V6, multiclass
[1] "Remove cluster labels:" "3Q LOSS CNV"           
clus
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                2               107 
       TCGA-06-0650        TCGA-06-1804        TCGA-06-1806        TCGA-06-5408 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-6388        TCGA-06-6389 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-06-6390        TCGA-06-6391        TCGA-06-6693        TCGA-06-6694 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-06-6695        TCGA-06-6697        TCGA-06-6698        TCGA-06-6699 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-06-6700        TCGA-06-6701        TCGA-12-5295        TCGA-12-5299 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-12-5301        TCGA-14-0740        TCGA-14-0781        TCGA-14-0862 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-14-1043        TCGA-14-1395        TCGA-14-1450        TCGA-15-1444 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-19-4065        TCGA-19-5947        TCGA-19-5950        TCGA-19-5951 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-19-5952        TCGA-19-5953        TCGA-19-5954        TCGA-19-5955 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-19-5956        TCGA-19-5958        TCGA-19-5959        TCGA-19-5960 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-26-6173 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-26-6174        TCGA-28-2501        TCGA-28-2510        TCGA-28-5204 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-28-5207        TCGA-28-5208        TCGA-28-5209        TCGA-28-5211 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-28-5213        TCGA-28-5214        TCGA-28-5215        TCGA-28-5216 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5219        TCGA-28-5220        TCGA-28-6450 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-32-1979        TCGA-32-1980        TCGA-32-5222        TCGA-41-5651 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4925 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-76-4926        TCGA-76-4928        TCGA-76-4931        TCGA-76-4934 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-76-4935        TCGA-76-6191        TCGA-76-6192        TCGA-76-6193 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-76-6280        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-76-6286        TCGA-76-6656        TCGA-76-6657        TCGA-76-6660 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-76-6661        TCGA-76-6662        TCGA-76-6663        TCGA-76-6664 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-81-5910        TCGA-81-5911        TCGA-87-5896 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
D45V7, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           2                52
  CLUS_2           1                57
  CLUS_3           2                42
  CLUS_4           2                43
D45V8, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           2                62
  CLUS_2           1                32
  CLUS_3           4               100
D45V9, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           2                42
  CLUS_2           1                66
  CLUS_3           0                36
D45V10, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           2                64
  CLUS_2           1                20
  CLUS_3           0                60

Clustering(46) Variable = 4p loss
D46V1, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           3               144
  CLUS_2           9                87
  CLUS_3           7               145
  CLUS_4           5               108
D46V2, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           3               114
  CLUS_2          14               157
  CLUS_3           7               213
D46V3, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           3               136
  CLUS_2          12               143
  CLUS_3           4                69
  CLUS_4           5                99
D46V4, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           7               174
  CLUS_2           5               150
  CLUS_3          12               123
D46V5, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           7               154
  CLUS_2          10               178
  CLUS_3           9               203
D46V6, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           2                37
  CLUS_2           2                25
  CLUS_3           0                16
  CLUS_4           0                27
D46V7, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           1                53
  CLUS_2           2                56
  CLUS_3           6                38
  CLUS_4           3                42
D46V8, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           6                58
  CLUS_2           1                32
  CLUS_3           5                99
D46V9, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           0                44
  CLUS_2           3                64
  CLUS_3           3                33
D46V10, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           4                62
  CLUS_2           1                20
  CLUS_3           1                59

Clustering(47) Variable = 4q loss
D47V1, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           3               144
  CLUS_2          12                84
  CLUS_3           3               149
  CLUS_4           4               109
D47V2, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           3               114
  CLUS_2          12               159
  CLUS_3           7               213
D47V3, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           2               137
  CLUS_2          10               145
  CLUS_3           4                69
  CLUS_4           5                99
D47V4, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           6               175
  CLUS_2           5               150
  CLUS_3          10               125
D47V5, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1          11               150
  CLUS_2           9               179
  CLUS_3           5               207
D47V6, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           1                38
  CLUS_2           1                26
  CLUS_3           0                16
  CLUS_4           2                25
D47V7, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           1                53
  CLUS_2           1                57
  CLUS_3           5                39
  CLUS_4           3                42
D47V8, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           5                59
  CLUS_2           1                32
  CLUS_3           4               100
D47V9, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           2                42
  CLUS_2           1                66
  CLUS_3           2                34
D47V10, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           3                63
  CLUS_2           1                20
  CLUS_3           1                59

Clustering(48) Variable = 5p loss
D48V1, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           1               146
  CLUS_2          11                85
  CLUS_3           6               146
  CLUS_4           2               111
D48V2, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           7               110
  CLUS_2           9               162
  CLUS_3           4               216
D48V3, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           3               136
  CLUS_2          11               144
  CLUS_3           2                71
  CLUS_4           3               101
D48V4, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           7               174
  CLUS_2           3               152
  CLUS_3           9               126
D48V5, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           6               155
  CLUS_2          11               177
  CLUS_3           4               208
D48V6, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           0                39
  CLUS_2           0                27
  CLUS_3           1                15
  CLUS_4           3                24
D48V7, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           4                50
  CLUS_2           1                57
  CLUS_3           3                41
  CLUS_4           2                43
D48V8, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           3                61
  CLUS_2           1                32
  CLUS_3           6                98
D48V9, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           3                41
  CLUS_2           3                64
  CLUS_3           1                35
D48V10, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           3                63
  CLUS_2           2                19
  CLUS_3           2                58

Clustering(49) Variable = 5q loss
D49V1, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           2               145
  CLUS_2          10                86
  CLUS_3           5               147
  CLUS_4           2               111
D49V2, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           5               112
  CLUS_2           7               164
  CLUS_3           7               213
D49V3, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           3               136
  CLUS_2          10               145
  CLUS_3           2                71
  CLUS_4           3               101
D49V4, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           5               176
  CLUS_2           4               151
  CLUS_3           9               126
D49V5, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           6               155
  CLUS_2          11               177
  CLUS_3           3               209
D49V6, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           0                39
  CLUS_2           0                27
  CLUS_3           1                15
  CLUS_4           3                24
D49V7, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           3                51
  CLUS_2           2                56
  CLUS_3           3                41
  CLUS_4           2                43
D49V8, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           3                61
  CLUS_2           1                32
  CLUS_3           6                98
D49V9, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           4                40
  CLUS_2           3                64
  CLUS_3           1                35
D49V10, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           4                62
  CLUS_2           2                19
  CLUS_3           2                58

Clustering(50) Variable = 6p loss
D50V1, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1          13               134
  CLUS_2           7                89
  CLUS_3          12               140
  CLUS_4          11               102
D50V2, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1          11               106
  CLUS_2          17               154
  CLUS_3          15               205
D50V3, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1          13               126
  CLUS_2          17               138
  CLUS_3           5                68
  CLUS_4           5                99
D50V4, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1          19               162
  CLUS_2          10               145
  CLUS_3          11               124
D50V5, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1          33               128
  CLUS_2           8               180
  CLUS_3           5               207
D50V6, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           2                37
  CLUS_2           3                24
  CLUS_3           2                14
  CLUS_4           2                25
D50V7, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           6                48
  CLUS_2           5                53
  CLUS_3           3                41
  CLUS_4           4                41
D50V8, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           4                60
  CLUS_2           4                29
  CLUS_3          10                94
D50V9, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           5                39
  CLUS_2           6                61
  CLUS_3           5                31
D50V10, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           5                61
  CLUS_2           2                19
  CLUS_3           9                51

Clustering(51) Variable = 6q loss
D51V1, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          21               126
  CLUS_2          13                83
  CLUS_3          25               127
  CLUS_4          16                97
D51V2, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          20                97
  CLUS_2          26               145
  CLUS_3          29               191
D51V3, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          24               115
  CLUS_2          23               132
  CLUS_3           9                64
  CLUS_4          12                92
D51V4, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          35               146
  CLUS_2          17               138
  CLUS_3          16               119
D51V5, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          47               114
  CLUS_2          12               176
  CLUS_3          21               191
D51V6, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           3                36
  CLUS_2           6                21
  CLUS_3           6                10
  CLUS_4           3                24
D51V7, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           8                46
  CLUS_2           6                52
  CLUS_3           6                38
  CLUS_4           5                40
D51V8, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           9                55
  CLUS_2           5                28
  CLUS_3          11                93
D51V9, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           7                37
  CLUS_2          14                53
  CLUS_3           6                30
D51V10, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          12                54
  CLUS_2           6                15
  CLUS_3           9                51

Clustering(52) Variable = 7p loss
D52V1, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           0               147
  CLUS_2           2                94
  CLUS_3           1               151
  CLUS_4           2               111
D52V2, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           1               116
  CLUS_2           3               168
  CLUS_3           1               219
D52V3, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           1               138
  CLUS_2           3               152
  CLUS_3           0                73
  CLUS_4           1               103
D52V4, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           1               180
  CLUS_2           0               155
  CLUS_3           4               131
D52V5, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           1               160
  CLUS_2           3               185
  CLUS_3           1               211
D52V6, multiclass
D52V7, multiclass
D52V8, multiclass
D52V9, multiclass
D52V10, multiclass

Clustering(53) Variable = 7q loss
D53V1, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           0               147
  CLUS_2           2                94
  CLUS_3           1               151
  CLUS_4           1               112
D53V2, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           1               116
  CLUS_2           2               169
  CLUS_3           1               219
D53V3, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           1               138
  CLUS_2           2               153
  CLUS_3           0                73
  CLUS_4           1               103
D53V4, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           1               180
  CLUS_2           0               155
  CLUS_3           3               132
D53V5, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           1               160
  CLUS_2           2               186
  CLUS_3           1               211
D53V6, multiclass
D53V7, multiclass
D53V8, multiclass
D53V9, multiclass
D53V10, multiclass

Clustering(54) Variable = 8p loss
D54V1, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          12               135
  CLUS_2           3                93
  CLUS_3          11               141
  CLUS_4           5               108
D54V2, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           6               111
  CLUS_2          10               161
  CLUS_3          15               205
D54V3, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          11               128
  CLUS_2          10               145
  CLUS_3           3                70
  CLUS_4           6                98
D54V4, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          16               165
  CLUS_2           8               147
  CLUS_3           6               129
D54V5, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          14               147
  CLUS_2           9               179
  CLUS_3          11               201
D54V6, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           2                37
  CLUS_2           1                26
  CLUS_3           2                14
  CLUS_4           0                27
D54V7, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           4                50
  CLUS_2           2                56
  CLUS_3           1                43
  CLUS_4           3                42
D54V8, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           3                61
  CLUS_2           2                31
  CLUS_3           5                99
D54V9, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           2                42
  CLUS_2           5                62
  CLUS_3           1                35
D54V10, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           5                61
  CLUS_2           1                20
  CLUS_3           2                58

Clustering(55) Variable = 8q loss
D55V1, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           8               139
  CLUS_2           2                94
  CLUS_3           7               145
  CLUS_4           3               110
D55V2, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           3               114
  CLUS_2           5               166
  CLUS_3          12               208
D55V3, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           9               130
  CLUS_2           4               151
  CLUS_3           2                71
  CLUS_4           4               100
D55V4, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1          10               171
  CLUS_2           7               148
  CLUS_3           2               133
D55V5, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1          12               149
  CLUS_2           3               185
  CLUS_3           6               206
D55V6, multiclass
[1] "Remove cluster labels:" "8Q LOSS CNV"           
clus
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                2               107 
       TCGA-06-0650        TCGA-06-1804        TCGA-06-1806        TCGA-06-5410 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-06-5411        TCGA-06-5412        TCGA-06-5413        TCGA-06-5414 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-06-5415        TCGA-06-5416        TCGA-06-5418        TCGA-06-5856 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-06-5858        TCGA-06-5859        TCGA-06-6388        TCGA-06-6389 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-06-6390        TCGA-06-6391        TCGA-06-6693        TCGA-06-6694 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-06-6695        TCGA-06-6697        TCGA-06-6698        TCGA-06-6699 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-06-6700        TCGA-06-6701        TCGA-12-5295        TCGA-12-5299 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-12-5301        TCGA-14-0740        TCGA-14-0781        TCGA-14-0862 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-14-1043        TCGA-14-1395        TCGA-15-1444        TCGA-19-4065 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-19-5947        TCGA-19-5950        TCGA-19-5951        TCGA-19-5952 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-19-5953        TCGA-19-5954        TCGA-19-5955        TCGA-19-5956 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-19-5958        TCGA-19-5959        TCGA-19-5960        TCGA-26-1442 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-26-5132        TCGA-26-5133        TCGA-26-5134        TCGA-26-5135 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-26-5136        TCGA-26-5139        TCGA-26-6173        TCGA-26-6174 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-28-2501        TCGA-28-2510        TCGA-28-5204        TCGA-28-5207 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-28-5208        TCGA-28-5209        TCGA-28-5211        TCGA-28-5213 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-28-5214        TCGA-28-5215        TCGA-28-5216        TCGA-28-5218 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-28-5219        TCGA-28-5220        TCGA-28-6450        TCGA-32-1979 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-32-1980        TCGA-32-5222        TCGA-41-5651        TCGA-41-6646 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-74-6573        TCGA-74-6575        TCGA-74-6577        TCGA-74-6578 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-74-6581        TCGA-74-6584        TCGA-76-4925        TCGA-76-4926 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-4934 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-76-4935        TCGA-76-6191        TCGA-76-6192        TCGA-76-6193 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-76-6280        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-76-6286        TCGA-76-6656        TCGA-76-6657        TCGA-76-6660 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-76-6661        TCGA-76-6662        TCGA-76-6663        TCGA-76-6664 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-81-5910        TCGA-81-5911        TCGA-87-5896 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D55V7, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           2                52
  CLUS_2           0                58
  CLUS_3           0                44
  CLUS_4           2                43
D55V8, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           1                63
  CLUS_2           1                32
  CLUS_3           2               102
D55V9, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           1                43
  CLUS_2           3                64
  CLUS_3           1                35
D55V10, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           4                62
  CLUS_2           0                21
  CLUS_3           1                59

Clustering(56) Variable = 9p loss
D56V1, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          40               107
  CLUS_2          16                80
  CLUS_3          58                94
  CLUS_4          37                76
D56V2, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          47                70
  CLUS_2          40               131
  CLUS_3          64               156
D56V3, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          42                97
  CLUS_2          43               112
  CLUS_3          22                51
  CLUS_4          34                70
D56V4, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          64               117
  CLUS_2          44               111
  CLUS_3          33               102
D56V5, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          46               115
  CLUS_2          48               140
  CLUS_3          71               141
D56V6, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          11                28
  CLUS_2           9                18
  CLUS_3           4                12
  CLUS_4           6                21
D56V7, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          20                34
  CLUS_2          13                45
  CLUS_3          17                27
  CLUS_4          16                29
D56V8, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          28                36
  CLUS_2          12                21
  CLUS_3          26                78
D56V9, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           7                37
  CLUS_2          21                46
  CLUS_3          15                21
D56V10, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          15                51
  CLUS_2          11                10
  CLUS_3          17                43

Clustering(57) Variable = 9q loss
D57V1, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          16               131
  CLUS_2           8                88
  CLUS_3          24               128
  CLUS_4          11               102
D57V2, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          24                93
  CLUS_2          12               159
  CLUS_3          23               197
D57V3, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          16               123
  CLUS_2          20               135
  CLUS_3           6                67
  CLUS_4          14                90
D57V4, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          28               153
  CLUS_2          18               137
  CLUS_3          10               125
D57V5, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          26               135
  CLUS_2          14               174
  CLUS_3          24               188
D57V6, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           2                37
  CLUS_2           2                25
  CLUS_3           1                15
  CLUS_4           4                23
D57V7, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           7                47
  CLUS_2           1                57
  CLUS_3           8                36
  CLUS_4           6                39
D57V8, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          12                52
  CLUS_2           4                29
  CLUS_3           6                98
D57V9, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           4                40
  CLUS_2          11                56
  CLUS_3           3                33
D57V10, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           8                58
  CLUS_2           5                16
  CLUS_3           5                55

Clustering(58) Variable = 10p loss
D58V1, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1          116                 31
  CLUS_2           61                 35
  CLUS_3          138                 14
  CLUS_4           76                 37
D58V2, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1          105                 12
  CLUS_2          115                 56
  CLUS_3          171                 49
D58V3, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1          121                 18
  CLUS_2          115                 40
  CLUS_3           53                 20
  CLUS_4           79                 25
D58V4, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1          159                 22
  CLUS_2          129                 26
  CLUS_3           80                 55
D58V5, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1          137                 24
  CLUS_2           94                 94
  CLUS_3          203                  9
D58V6, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1           28                 11
  CLUS_2           26                  1
  CLUS_3           16                  0
  CLUS_4           20                  7
D58V7, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1           43                 11
  CLUS_2           39                 19
  CLUS_3           43                  1
  CLUS_4           38                  7
D58V8, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1           61                  3
  CLUS_2           25                  8
  CLUS_3           77                 27
D58V9, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1           35                  9
  CLUS_2           56                 11
  CLUS_3           32                  4
D58V10, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1           54                 12
  CLUS_2           21                  0
  CLUS_3           48                 12

Clustering(59) Variable = 10q loss
D59V1, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1          117                 30
  CLUS_2           66                 30
  CLUS_3          143                  9
  CLUS_4           79                 34
D59V2, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1          110                  7
  CLUS_2          121                 50
  CLUS_3          174                 46
D59V3, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1          124                 15
  CLUS_2          123                 32
  CLUS_3           53                 20
  CLUS_4           82                 22
D59V4, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1          162                 19
  CLUS_2          130                 25
  CLUS_3           90                 45
D59V5, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1          140                 21
  CLUS_2           99                 89
  CLUS_3          208                  4
D59V6, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           28                 11
  CLUS_2           26                  1
  CLUS_3           16                  0
  CLUS_4           19                  8
D59V7, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           42                 12
  CLUS_2           40                 18
  CLUS_3           44                  0
  CLUS_4           39                  6
D59V8, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           61                  3
  CLUS_2           25                  8
  CLUS_3           79                 25
D59V9, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           36                  8
  CLUS_2           57                 10
  CLUS_3           32                  4
D59V10, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           55                 11
  CLUS_2           21                  0
  CLUS_3           49                 11

Clustering(60) Variable = 11p loss
D60V1, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1           12                135
  CLUS_2           28                 68
  CLUS_3            4                148
  CLUS_4           16                 97
D60V2, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            4                113
  CLUS_2           35                136
  CLUS_3           21                199
D60V3, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1           11                128
  CLUS_2           25                130
  CLUS_3            9                 64
  CLUS_4           13                 91
D60V4, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            9                172
  CLUS_2           17                138
  CLUS_3           32                103
D60V5, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1           37                124
  CLUS_2           23                165
  CLUS_3            3                209
D60V6, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            0                 39
  CLUS_2            1                 26
  CLUS_3            0                 16
  CLUS_4            6                 21
D60V7, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            8                 46
  CLUS_2            7                 51
  CLUS_3            3                 41
  CLUS_4            5                 40
D60V8, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            3                 61
  CLUS_2            3                 30
  CLUS_3           17                 87
D60V9, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1           10                 34
  CLUS_2            6                 61
  CLUS_3            2                 34
D60V10, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            6                 60
  CLUS_2            2                 19
  CLUS_3           10                 50

Clustering(61) Variable = 11q loss
D61V1, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1           15                132
  CLUS_2           22                 74
  CLUS_3            5                147
  CLUS_4           11                102
D61V2, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            5                112
  CLUS_2           27                144
  CLUS_3           21                199
D61V3, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1           12                127
  CLUS_2           18                137
  CLUS_3            9                 64
  CLUS_4           11                 93
D61V4, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1           10                171
  CLUS_2           19                136
  CLUS_3           21                114
D61V5, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1           35                126
  CLUS_2           15                173
  CLUS_3            4                208
D61V6, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            0                 39
  CLUS_2            1                 26
  CLUS_3            1                 15
  CLUS_4            2                 25
D61V7, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            6                 48
  CLUS_2            4                 54
  CLUS_3            2                 42
  CLUS_4            5                 40
D61V8, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            2                 62
  CLUS_2            2                 31
  CLUS_3           13                 91
D61V9, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            5                 39
  CLUS_2            8                 59
  CLUS_3            2                 34
D61V10, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            8                 58
  CLUS_2            2                 19
  CLUS_3            5                 55

Clustering(62) Variable = 12p loss
D62V1, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            9                138
  CLUS_2           13                 83
  CLUS_3            6                146
  CLUS_4            8                105
D62V2, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            3                114
  CLUS_2           19                152
  CLUS_3           14                206
D62V3, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1           12                127
  CLUS_2           15                140
  CLUS_3            6                 67
  CLUS_4            3                101
D62V4, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1           14                167
  CLUS_2            6                149
  CLUS_3           16                119
D62V5, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1           13                148
  CLUS_2           12                176
  CLUS_3           13                199
D62V6, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            2                 37
  CLUS_2            2                 25
  CLUS_3            1                 15
  CLUS_4            0                 27
D62V7, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            1                 53
  CLUS_2            4                 54
  CLUS_3            4                 40
  CLUS_4            0                 45
D62V8, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            4                 60
  CLUS_2            0                 33
  CLUS_3            5                 99
D62V9, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            3                 41
  CLUS_2            5                 62
  CLUS_3            2                 34
D62V10, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            5                 61
  CLUS_2            1                 20
  CLUS_3            4                 56

Clustering(63) Variable = 12q loss
D63V1, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            5                142
  CLUS_2           10                 86
  CLUS_3            7                145
  CLUS_4           10                103
D63V2, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            3                114
  CLUS_2           19                152
  CLUS_3           10                210
D63V3, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            9                130
  CLUS_2           13                142
  CLUS_3            4                 69
  CLUS_4            5                 99
D63V4, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1           10                171
  CLUS_2            6                149
  CLUS_3           15                120
D63V5, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1           15                146
  CLUS_2           11                177
  CLUS_3            9                203
D63V6, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            1                 38
  CLUS_2            3                 24
  CLUS_3            0                 16
  CLUS_4            2                 25
D63V7, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            2                 52
  CLUS_2            4                 54
  CLUS_3            5                 39
  CLUS_4            0                 45
D63V8, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            5                 59
  CLUS_2            1                 32
  CLUS_3            5                 99
D63V9, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            4                 40
  CLUS_2            4                 63
  CLUS_3            2                 34
D63V10, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            5                 61
  CLUS_2            0                 21
  CLUS_3            5                 55

Clustering(64) Variable = 13q loss
D64V1, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           45                102
  CLUS_2           28                 68
  CLUS_3           18                134
  CLUS_4           33                 80
D64V2, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           13                104
  CLUS_2           49                122
  CLUS_3           62                158
D64V3, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           36                103
  CLUS_2           38                117
  CLUS_3           23                 50
  CLUS_4           24                 80
D64V4, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           45                136
  CLUS_2           38                117
  CLUS_3           38                 97
D64V5, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           69                 92
  CLUS_2           50                138
  CLUS_3           19                193
D64V6, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            6                 33
  CLUS_2            4                 23
  CLUS_3            1                 15
  CLUS_4           14                 13
D64V7, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           14                 40
  CLUS_2           13                 45
  CLUS_3            7                 37
  CLUS_4           12                 33
D64V8, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            8                 56
  CLUS_2            6                 27
  CLUS_3           32                 72
D64V9, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           14                 30
  CLUS_2           12                 55
  CLUS_3            7                 29
D64V10, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           17                 49
  CLUS_2            2                 19
  CLUS_3           14                 46

Clustering(65) Variable = 14q loss
D65V1, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           38                109
  CLUS_2           31                 65
  CLUS_3           13                139
  CLUS_4           32                 81
D65V2, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           15                102
  CLUS_2           49                122
  CLUS_3           50                170
D65V3, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           26                113
  CLUS_2           40                115
  CLUS_3           18                 55
  CLUS_4           21                 83
D65V4, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           44                137
  CLUS_2           34                121
  CLUS_3           27                108
D65V5, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           84                 77
  CLUS_2           32                156
  CLUS_3            4                208
D65V6, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            8                 31
  CLUS_2            6                 21
  CLUS_3            0                 16
  CLUS_4           11                 16
D65V7, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           13                 41
  CLUS_2           14                 44
  CLUS_3            7                 37
  CLUS_4           10                 35
D65V8, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            8                 56
  CLUS_2            7                 26
  CLUS_3           29                 75
D65V9, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           19                 25
  CLUS_2           14                 53
  CLUS_3            9                 27
D65V10, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           17                 49
  CLUS_2            1                 20
  CLUS_3           24                 36

Clustering(66) Variable = 15q loss
D66V1, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           16                131
  CLUS_2           16                 80
  CLUS_3            7                145
  CLUS_4           20                 93
D66V2, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            3                114
  CLUS_2           33                138
  CLUS_3           23                197
D66V3, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            9                130
  CLUS_2           27                128
  CLUS_3           13                 60
  CLUS_4            6                 98
D66V4, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           19                162
  CLUS_2            6                149
  CLUS_3           30                105
D66V5, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           35                126
  CLUS_2           14                174
  CLUS_3           13                199
D66V6, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            1                 38
  CLUS_2            2                 25
  CLUS_3            0                 16
  CLUS_4            9                 18
D66V7, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            8                 46
  CLUS_2           13                 45
  CLUS_3            3                 41
  CLUS_4            4                 41
D66V8, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            3                 61
  CLUS_2            5                 28
  CLUS_3           20                 84
D66V9, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           12                 32
  CLUS_2            7                 60
  CLUS_3            2                 34
D66V10, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           11                 55
  CLUS_2            1                 20
  CLUS_3            9                 51

Clustering(67) Variable = 16p loss
D67V1, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            8                139
  CLUS_2            8                 88
  CLUS_3            4                148
  CLUS_4            3                110
D67V2, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            3                114
  CLUS_2            9                162
  CLUS_3           11                209
D67V3, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            6                133
  CLUS_2            6                149
  CLUS_3            2                 71
  CLUS_4            8                 96
D67V4, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            7                174
  CLUS_2            9                146
  CLUS_3            6                129
D67V5, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1           11                150
  CLUS_2            5                183
  CLUS_3            7                205
D67V6, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            0                 39
  CLUS_2            1                 26
  CLUS_3            1                 15
  CLUS_4            1                 26
D67V7, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            2                 52
  CLUS_2            1                 57
  CLUS_3            2                 42
  CLUS_4            3                 42
D67V8, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            2                 62
  CLUS_2            1                 32
  CLUS_3            5                 99
D67V9, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            2                 42
  CLUS_2            6                 61
  CLUS_3            1                 35
D67V10, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            4                 62
  CLUS_2            3                 18
  CLUS_3            2                 58

Clustering(68) Variable = 16q loss
D68V1, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           15                132
  CLUS_2           10                 86
  CLUS_3            5                147
  CLUS_4            8                105
D68V2, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            4                113
  CLUS_2           12                159
  CLUS_3           22                198
D68V3, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           14                125
  CLUS_2            8                147
  CLUS_3            3                 70
  CLUS_4           12                 92
D68V4, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           12                169
  CLUS_2           16                139
  CLUS_3            9                126
D68V5, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           16                145
  CLUS_2           13                175
  CLUS_3           12                200
D68V6, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            1                 38
  CLUS_2            3                 24
  CLUS_3            2                 14
  CLUS_4            2                 25
D68V7, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            7                 47
  CLUS_2            1                 57
  CLUS_3            4                 40
  CLUS_4            6                 39
D68V8, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            5                 59
  CLUS_2            3                 30
  CLUS_3           10                 94
D68V9, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            4                 40
  CLUS_2            7                 60
  CLUS_3            2                 34
D68V10, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            6                 60
  CLUS_2            3                 18
  CLUS_3            4                 56

Clustering(69) Variable = 17p loss
D69V1, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           11                136
  CLUS_2            9                 87
  CLUS_3            4                148
  CLUS_4            8                105
D69V2, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            6                111
  CLUS_2           14                157
  CLUS_3           12                208
D69V3, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            9                130
  CLUS_2           12                143
  CLUS_3            5                 68
  CLUS_4            5                 99
D69V4, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           11                170
  CLUS_2           10                145
  CLUS_3           10                125
D69V5, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           20                141
  CLUS_2           14                174
  CLUS_3            2                210
D69V6, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            2                 37
  CLUS_2            2                 25
  CLUS_3            0                 16
  CLUS_4            4                 23
D69V7, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            7                 47
  CLUS_2            6                 52
  CLUS_3            3                 41
  CLUS_4            0                 45
D69V8, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            4                 60
  CLUS_2            3                 30
  CLUS_3            9                 95
D69V9, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            2                 42
  CLUS_2            6                 61
  CLUS_3            4                 32
D69V10, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            6                 60
  CLUS_2            1                 20
  CLUS_3            5                 55

Clustering(70) Variable = 17q loss
D70V1, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            8                139
  CLUS_2            4                 92
  CLUS_3            4                148
  CLUS_4            1                112
D70V2, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            5                112
  CLUS_2            3                168
  CLUS_3            9                211
D70V3, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            8                131
  CLUS_2            4                151
  CLUS_3            1                 72
  CLUS_4            4                100
D70V4, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            8                173
  CLUS_2            7                148
  CLUS_3            2                133
D70V5, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1           11                150
  CLUS_2            7                181
  CLUS_3            1                211
D70V6, multiclass
[1] "Remove cluster labels:" "17Q LOSS CNV"          
clus
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 2                107 
        TCGA-06-0650         TCGA-06-1804         TCGA-06-1806 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5299         TCGA-12-5301 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-14-0740         TCGA-14-0781         TCGA-14-0862 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-14-1043         TCGA-14-1395         TCGA-14-1450 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-15-1444         TCGA-19-5947         TCGA-19-5950 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-19-5951         TCGA-19-5952         TCGA-19-5953 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-19-5954         TCGA-19-5955         TCGA-19-5956 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-19-5958         TCGA-19-5959         TCGA-19-5960 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-26-1442         TCGA-26-5132         TCGA-26-5133 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-26-5134         TCGA-26-5135         TCGA-26-5136 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-26-5139         TCGA-26-6173         TCGA-26-6174 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-28-2501         TCGA-28-2510         TCGA-28-5204 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-28-5211         TCGA-28-5213         TCGA-28-5214 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-28-5215         TCGA-28-5216         TCGA-28-5218 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-28-5219         TCGA-28-5220         TCGA-28-6450 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-32-1979         TCGA-32-1980         TCGA-32-5222 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-41-5651         TCGA-41-6646         TCGA-74-6573 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-74-6575         TCGA-74-6577         TCGA-74-6578 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-74-6581         TCGA-74-6584         TCGA-76-4925 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-76-4931         TCGA-76-4934         TCGA-76-4935 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-76-6191         TCGA-76-6192         TCGA-76-6193 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-76-6280         TCGA-76-6282         TCGA-76-6283 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-76-6286         TCGA-76-6656         TCGA-76-6657 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-76-6660         TCGA-76-6661         TCGA-76-6662 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-76-6663         TCGA-76-6664         TCGA-81-5910 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-81-5911         TCGA-87-5896 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
D70V7, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            3                 51
  CLUS_2            1                 57
  CLUS_3            3                 41
  CLUS_4            0                 45
D70V8, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            4                 60
  CLUS_2            1                 32
  CLUS_3            2                102
D70V9, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            0                 44
  CLUS_2            5                 62
  CLUS_3            1                 35
D70V10, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            5                 61
  CLUS_2            1                 20
  CLUS_3            0                 60

Clustering(71) Variable = 18p loss
D71V1, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           11                136
  CLUS_2           15                 81
  CLUS_3            4                148
  CLUS_4            7                106
D71V2, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            3                114
  CLUS_2           16                155
  CLUS_3           18                202
D71V3, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            8                131
  CLUS_2           14                141
  CLUS_3            3                 70
  CLUS_4            9                 95
D71V4, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           11                170
  CLUS_2           11                144
  CLUS_3           12                123
D71V5, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           22                139
  CLUS_2           15                173
  CLUS_3            7                205
D71V6, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            3                 36
  CLUS_2            4                 23
  CLUS_3            1                 15
  CLUS_4            7                 20
D71V7, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            5                 49
  CLUS_2            7                 51
  CLUS_3            1                 43
  CLUS_4            6                 39
D71V8, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            2                 62
  CLUS_2            2                 31
  CLUS_3           15                 89
D71V9, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            7                 37
  CLUS_2            3                 64
  CLUS_3            1                 35
D71V10, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            6                 60
  CLUS_2            0                 21
  CLUS_3            5                 55

Clustering(72) Variable = 18q loss
D72V1, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            9                138
  CLUS_2           10                 86
  CLUS_3            6                146
  CLUS_4            8                105
D72V2, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            3                114
  CLUS_2           13                158
  CLUS_3           17                203
D72V3, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           13                126
  CLUS_2           10                145
  CLUS_3            2                 71
  CLUS_4            7                 97
D72V4, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           13                168
  CLUS_2           10                145
  CLUS_3            9                126
D72V5, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           16                145
  CLUS_2           14                174
  CLUS_3            8                204
D72V6, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            2                 37
  CLUS_2            3                 24
  CLUS_3            0                 16
  CLUS_4            5                 22
D72V7, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            3                 51
  CLUS_2            8                 50
  CLUS_3            0                 44
  CLUS_4            5                 40
D72V8, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            0                 64
  CLUS_2            1                 32
  CLUS_3           15                 89
D72V9, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            5                 39
  CLUS_2            4                 63
  CLUS_3            2                 34
D72V10, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            4                 62
  CLUS_2            1                 20
  CLUS_3            6                 54

Clustering(73) Variable = 19p loss
D73V1, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                146
  CLUS_2            7                 89
  CLUS_3            0                152
  CLUS_4            3                110
D73V2, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            0                117
  CLUS_2            7                164
  CLUS_3            4                216
D73V3, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                138
  CLUS_2           10                145
  CLUS_3            0                 73
  CLUS_4            0                104
D73V4, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            5                176
  CLUS_2            0                155
  CLUS_3            6                129
D73V5, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            7                154
  CLUS_2            3                185
  CLUS_3            2                210
D73V6, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                 38
  CLUS_2            0                 27
  CLUS_3            0                 16
  CLUS_4            2                 25
D73V7, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            0                 54
  CLUS_2            3                 55
  CLUS_3            1                 43
  CLUS_4            1                 44
D73V8, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                 63
  CLUS_2            0                 33
  CLUS_3            4                100
D73V9, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            2                 42
  CLUS_2            1                 66
  CLUS_3            0                 36
D73V10, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            3                 63
  CLUS_2            0                 21
  CLUS_3            0                 60

Clustering(74) Variable = 19q loss
D74V1, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            3                144
  CLUS_2            6                 90
  CLUS_3            0                152
  CLUS_4            6                107
D74V2, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            1                116
  CLUS_2            8                163
  CLUS_3            6                214
D74V3, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            1                138
  CLUS_2           10                145
  CLUS_3            1                 72
  CLUS_4            3                101
D74V4, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            6                175
  CLUS_2            1                154
  CLUS_3            8                127
D74V5, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            8                153
  CLUS_2            6                182
  CLUS_3            2                210
D74V6, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            1                 38
  CLUS_2            0                 27
  CLUS_3            0                 16
  CLUS_4            2                 25
D74V7, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            0                 54
  CLUS_2            3                 55
  CLUS_3            1                 43
  CLUS_4            1                 44
D74V8, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            1                 63
  CLUS_2            0                 33
  CLUS_3            4                100
D74V9, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            2                 42
  CLUS_2            1                 66
  CLUS_3            1                 35
D74V10, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            3                 63
  CLUS_2            0                 21
  CLUS_3            1                 59

Clustering(75) Variable = 20p loss
D75V1, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            3                144
  CLUS_2            6                 90
  CLUS_3            0                152
  CLUS_4            1                112
D75V2, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            0                117
  CLUS_2            5                166
  CLUS_3            5                215
D75V3, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            1                138
  CLUS_2            4                151
  CLUS_3            4                 69
  CLUS_4            1                103
D75V4, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            3                178
  CLUS_2            1                154
  CLUS_3            6                129
D75V5, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            7                154
  CLUS_2            4                184
  CLUS_3            0                212
D75V6, multiclass
[1] "Remove cluster labels:" "20P LOSS CNV"          
clus
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 1                108 
        TCGA-06-0650         TCGA-06-1804         TCGA-06-1806 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5299         TCGA-12-5301 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-14-0740         TCGA-14-0781         TCGA-14-0862 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-14-1043         TCGA-14-1395         TCGA-14-1450 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-15-1444         TCGA-19-4065         TCGA-19-5947 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-19-5950         TCGA-19-5951         TCGA-19-5952 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-19-5953         TCGA-19-5954         TCGA-19-5955 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-19-5956         TCGA-19-5958         TCGA-19-5959 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-26-5136         TCGA-26-5139         TCGA-26-6173 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-26-6174         TCGA-28-2501         TCGA-28-2510 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5211         TCGA-28-5213 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-5214         TCGA-28-5215         TCGA-28-5216 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-5218         TCGA-28-5219         TCGA-28-5220 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-6450         TCGA-32-1979         TCGA-32-1980 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-32-5222         TCGA-41-5651         TCGA-41-6646 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-74-6573         TCGA-74-6575         TCGA-74-6577 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-74-6578         TCGA-74-6581         TCGA-74-6584 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-76-4925         TCGA-76-4926         TCGA-76-4928 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931         TCGA-76-4934 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-76-4935         TCGA-76-6191         TCGA-76-6192 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-76-6193         TCGA-76-6280         TCGA-76-6282 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-76-6283         TCGA-76-6285         TCGA-76-6656 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-76-6657         TCGA-76-6660         TCGA-76-6661 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-76-6662         TCGA-76-6663         TCGA-76-6664 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-81-5910         TCGA-81-5911         TCGA-87-5896 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
D75V7, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            2                 52
  CLUS_2            2                 56
  CLUS_3            0                 44
  CLUS_4            0                 45
D75V8, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            0                 64
  CLUS_2            1                 32
  CLUS_3            3                101
D75V9, multiclass
[1] "Remove cluster labels:" "20P LOSS CNV"          
clus
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2569         TCGA-06-2570 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-08-0386         TCGA-12-0616         TCGA-12-0618 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-12-0619         TCGA-12-0821         TCGA-12-3650 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-12-5299         TCGA-14-0781         TCGA-14-0787 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-14-0789         TCGA-14-0790         TCGA-14-0817 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-14-1034         TCGA-14-1823         TCGA-14-1825 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-14-1829         TCGA-14-2554         TCGA-15-0742 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-15-1444         TCGA-16-0846         TCGA-16-1045 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2620 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-19-2624         TCGA-19-2625         TCGA-19-4065 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-26-5136         TCGA-26-5139         TCGA-27-1830 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1834 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-27-1835         TCGA-27-1837         TCGA-27-2519 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-27-2521         TCGA-27-2523         TCGA-27-2524 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-27-2526         TCGA-27-2528         TCGA-28-1747 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-1753         TCGA-28-2509         TCGA-28-2510 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-2513         TCGA-28-2514         TCGA-28-5204 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-5213         TCGA-28-5215         TCGA-28-5216 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-5218         TCGA-28-5220         TCGA-32-1970 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-76-4931 
"20P LOSS WILD-TYPE" 
D75V10, multiclass
[1] "Remove cluster labels:" "20P LOSS CNV"          
clus
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2569         TCGA-06-2570 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-08-0386         TCGA-12-0616         TCGA-12-0618 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-12-0619         TCGA-12-0821         TCGA-12-3650 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-12-5299         TCGA-14-0781         TCGA-14-0787 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-14-0789         TCGA-14-0790         TCGA-14-0817 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-14-1034         TCGA-14-1823         TCGA-14-1825 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-14-1829         TCGA-14-2554         TCGA-15-0742 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-15-1444         TCGA-16-0846         TCGA-16-1045 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2620 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-19-2624         TCGA-19-2625         TCGA-19-4065 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-26-5136         TCGA-26-5139         TCGA-27-1830 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1834 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-27-1835         TCGA-27-1837         TCGA-27-2519 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-27-2521         TCGA-27-2523         TCGA-27-2524 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-27-2526         TCGA-27-2528         TCGA-28-1747 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-1753         TCGA-28-2509         TCGA-28-2510 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-2513         TCGA-28-2514         TCGA-28-5204 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-5213         TCGA-28-5215         TCGA-28-5216 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-5218         TCGA-28-5220         TCGA-32-1970 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-76-4931 
"20P LOSS WILD-TYPE" 

Clustering(76) Variable = 20q loss
D76V1, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            3                144
  CLUS_2            5                 91
  CLUS_3            0                152
  CLUS_4            1                112
D76V2, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            0                117
  CLUS_2            5                166
  CLUS_3            4                216
D76V3, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            1                138
  CLUS_2            3                152
  CLUS_3            2                 71
  CLUS_4            2                102
D76V4, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            2                179
  CLUS_2            2                153
  CLUS_3            4                131
D76V5, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            7                154
  CLUS_2            2                186
  CLUS_3            1                211
D76V6, multiclass
[1] "Remove cluster labels:" "20Q LOSS CNV"          
clus
      20Q LOSS CNV 20Q LOSS WILD-TYPE 
                 2                107 
        TCGA-06-0650         TCGA-06-1804         TCGA-06-1806 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5299         TCGA-12-5301 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-14-0740         TCGA-14-0781         TCGA-14-0862 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-14-1043         TCGA-14-1395         TCGA-14-1450 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-15-1444         TCGA-19-4065         TCGA-19-5947 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-19-5950         TCGA-19-5951         TCGA-19-5952 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-19-5953         TCGA-19-5954         TCGA-19-5955 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-19-5956         TCGA-19-5958         TCGA-19-5959 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-26-5136         TCGA-26-5139         TCGA-26-6173 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-26-6174         TCGA-28-2501         TCGA-28-2510 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5211         TCGA-28-5213 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-5214         TCGA-28-5215         TCGA-28-5216 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-5218         TCGA-28-5219         TCGA-28-5220 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-6450         TCGA-32-1979         TCGA-32-1980 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-32-5222         TCGA-41-5651         TCGA-41-6646 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-74-6573         TCGA-74-6575         TCGA-74-6577 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-74-6578         TCGA-74-6581         TCGA-74-6584 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-76-4925         TCGA-76-4926         TCGA-76-4928 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931         TCGA-76-4934 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-76-4935         TCGA-76-6191         TCGA-76-6192 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-76-6193         TCGA-76-6280         TCGA-76-6282 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-76-6283         TCGA-76-6656         TCGA-76-6657 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-76-6660         TCGA-76-6661         TCGA-76-6662 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-76-6663         TCGA-76-6664         TCGA-81-5910 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-81-5911         TCGA-87-5896 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D76V7, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            2                 52
  CLUS_2            2                 56
  CLUS_3            0                 44
  CLUS_4            0                 45
D76V8, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            0                 64
  CLUS_2            1                 32
  CLUS_3            3                101
D76V9, multiclass
[1] "Remove cluster labels:" "20Q LOSS CNV"          
clus
      20Q LOSS CNV 20Q LOSS WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2569         TCGA-06-2570 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-08-0386         TCGA-12-0616         TCGA-12-0618 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-12-0619         TCGA-12-0821         TCGA-12-3650 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-12-5299         TCGA-14-0781         TCGA-14-0787 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-14-0789         TCGA-14-0790         TCGA-14-0817 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-14-1034         TCGA-14-1823         TCGA-14-1825 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-14-1829         TCGA-14-2554         TCGA-15-0742 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-15-1444         TCGA-16-0846         TCGA-16-1045 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2620 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-19-2624         TCGA-19-2625         TCGA-19-4065 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-26-5136         TCGA-26-5139         TCGA-27-1830 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1834 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-27-1835         TCGA-27-1837         TCGA-27-2519 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-27-2521         TCGA-27-2523         TCGA-27-2524 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-27-2526         TCGA-27-2528         TCGA-28-1747 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-1753         TCGA-28-2509         TCGA-28-2510 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-2513         TCGA-28-2514         TCGA-28-5204 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-5213         TCGA-28-5215         TCGA-28-5216 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-5218         TCGA-28-5220         TCGA-32-1970 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-76-4931 
"20Q LOSS WILD-TYPE" 
D76V10, multiclass
[1] "Remove cluster labels:" "20Q LOSS CNV"          
clus
      20Q LOSS CNV 20Q LOSS WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2569         TCGA-06-2570 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-08-0386         TCGA-12-0616         TCGA-12-0618 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-12-0619         TCGA-12-0821         TCGA-12-3650 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-12-5299         TCGA-14-0781         TCGA-14-0787 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-14-0789         TCGA-14-0790         TCGA-14-0817 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-14-1034         TCGA-14-1823         TCGA-14-1825 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-14-1829         TCGA-14-2554         TCGA-15-0742 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-15-1444         TCGA-16-0846         TCGA-16-1045 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2620 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-19-2624         TCGA-19-2625         TCGA-19-4065 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-26-5136         TCGA-26-5139         TCGA-27-1830 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1834 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-27-1835         TCGA-27-1837         TCGA-27-2519 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-27-2521         TCGA-27-2523         TCGA-27-2524 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-27-2526         TCGA-27-2528         TCGA-28-1747 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-1753         TCGA-28-2509         TCGA-28-2510 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-2513         TCGA-28-2514         TCGA-28-5204 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-5213         TCGA-28-5215         TCGA-28-5216 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-5218         TCGA-28-5220         TCGA-32-1970 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-76-4931 
"20Q LOSS WILD-TYPE" 

Clustering(77) Variable = 21q loss
D77V1, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            1                146
  CLUS_2           12                 84
  CLUS_3            5                147
  CLUS_4            5                108
D77V2, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            4                113
  CLUS_2           14                157
  CLUS_3            5                215
D77V3, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            3                136
  CLUS_2           12                143
  CLUS_3            5                 68
  CLUS_4            3                101
D77V4, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            5                176
  CLUS_2            4                151
  CLUS_3           14                121
D77V5, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1           12                149
  CLUS_2            9                179
  CLUS_3            4                208
D77V6, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            0                 39
  CLUS_2            3                 24
  CLUS_3            0                 16
  CLUS_4            2                 25
D77V7, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            0                 54
  CLUS_2            3                 55
  CLUS_3            4                 40
  CLUS_4            0                 45
D77V8, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            4                 60
  CLUS_2            0                 33
  CLUS_3            3                101
D77V9, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            2                 42
  CLUS_2            3                 64
  CLUS_3            0                 36
D77V10, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            2                 64
  CLUS_2            1                 20
  CLUS_3            2                 58

Clustering(78) Variable = 22q loss
D78V1, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           41                106
  CLUS_2           24                 72
  CLUS_3           36                116
  CLUS_4           29                 84
D78V2, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           33                 84
  CLUS_2           41                130
  CLUS_3           56                164
D78V3, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           36                103
  CLUS_2           45                110
  CLUS_3           17                 56
  CLUS_4           22                 82
D78V4, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           44                137
  CLUS_2           40                115
  CLUS_3           36                 99
D78V5, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           60                101
  CLUS_2           37                151
  CLUS_3           43                169
D78V6, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           10                 29
  CLUS_2           11                 16
  CLUS_3            5                 11
  CLUS_4            5                 22
D78V7, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           13                 41
  CLUS_2           18                 40
  CLUS_3           15                 29
  CLUS_4           13                 32
D78V8, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           18                 46
  CLUS_2           10                 23
  CLUS_3           31                 73
D78V9, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           12                 32
  CLUS_2           18                 49
  CLUS_3           16                 20
D78V10, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           22                 44
  CLUS_2            6                 15
  CLUS_3           18                 42

Clustering(79) Variable = Xq loss
D79V1, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           1               146
  CLUS_2           2                94
  CLUS_3           4               148
  CLUS_4           4               109
D79V2, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           4               113
  CLUS_2           4               167
  CLUS_3           3               217
D79V3, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           1               138
  CLUS_2           4               151
  CLUS_3           4                69
  CLUS_4           1               103
D79V4, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           5               176
  CLUS_2           1               154
  CLUS_3           4               131
D79V5, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           6               155
  CLUS_2           3               185
  CLUS_3           2               210
D79V6, multiclass
[1] "Remove cluster labels:" "XQ LOSS CNV"           
clus
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                2               107 
       TCGA-06-0650        TCGA-06-1804        TCGA-06-1806        TCGA-06-5408 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-06-6388 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-06-6389        TCGA-06-6390        TCGA-06-6391        TCGA-06-6693 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-06-6694        TCGA-06-6695        TCGA-06-6697        TCGA-06-6698 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-06-6699        TCGA-06-6700        TCGA-06-6701        TCGA-12-5295 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-12-5299        TCGA-12-5301        TCGA-14-0740        TCGA-14-0781 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-14-0862        TCGA-14-1043        TCGA-14-1395        TCGA-14-1450 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-15-1444        TCGA-19-4065        TCGA-19-5950        TCGA-19-5951 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-19-5952        TCGA-19-5953        TCGA-19-5954        TCGA-19-5955 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-19-5956        TCGA-19-5958        TCGA-19-5959        TCGA-19-5960 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-26-6173 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-26-6174        TCGA-28-2501        TCGA-28-2510        TCGA-28-5204 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-28-5207        TCGA-28-5208        TCGA-28-5209        TCGA-28-5211 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-28-5213        TCGA-28-5214        TCGA-28-5215        TCGA-28-5216 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5219        TCGA-28-5220        TCGA-28-6450 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-32-1979        TCGA-32-1980        TCGA-32-5222        TCGA-41-5651 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4925 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-4934 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-76-4935        TCGA-76-6191        TCGA-76-6192        TCGA-76-6193 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-76-6280        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-76-6286        TCGA-76-6656        TCGA-76-6657        TCGA-76-6660 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-76-6661        TCGA-76-6662        TCGA-76-6663        TCGA-76-6664 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-81-5910        TCGA-81-5911        TCGA-87-5896 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D79V7, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           2                52
  CLUS_2           2                56
  CLUS_3           2                42
  CLUS_4           0                45
D79V8, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           2                62
  CLUS_2           2                31
  CLUS_3           2               102
D79V9, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           2                42
  CLUS_2           1                66
  CLUS_3           2                34
D79V10, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           1                65
  CLUS_2           1                20
  CLUS_3           3                57
                     V1                      V2                      V3 
            "MRNA_CNMF"    "MRNA_CHIERARCHICAL"              "MIR_CNMF" 
                     V4                      V5                      V6 
    "MIR_CHIERARCHICAL"               "CN_CNMF"      "METHLYATION_CNMF" 
                     V7                      V8                      V9 
            "RPPA_CNMF"    "RPPA_CHIERARCHICAL"          "MRNASEQ_CNMF" 
                    V10 
"MRNASEQ_CHIERARCHICAL" 
> q(save="no")
