
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Cluster_cnvarms_onlysig/broadinstitute.org/cancer.genome.analysis/00508/6/CNV2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Cluster_cnvarms_onlysig/broadinstitute.org/cancer.genome.analysis/00508/6/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/cnvarms2cluster/LUAD-TP/3143009/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/LUAD-TP/3145444/1.GDAC_mergedClustering.Finished/LUAD-TP.transferedmergedcluster.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=LUAD-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=LUAD-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=477, in cluster file=472, common to both=472
[1]  80 472
[1] "1p gain"
[1] 3
      1P GAIN CNV 1P GAIN WILD-TYPE 
               58               414 
      1P GAIN CNV 1P GAIN WILD-TYPE 
               58               414 
[1] "1q gain"
[1] 3
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
              177               295 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
              177               295 
[1] "2p gain"
[1] 3
      2P GAIN CNV 2P GAIN WILD-TYPE 
               50               422 
      2P GAIN CNV 2P GAIN WILD-TYPE 
               50               422 
[1] "2q gain"
[1] 3
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
               45               427 
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
               45               427 
[1] "3p gain"
[1] 3
      3P GAIN CNV 3P GAIN WILD-TYPE 
               13               459 
      3P GAIN CNV 3P GAIN WILD-TYPE 
               13               459 
[1] "3q gain"
[1] 3
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               29               443 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               29               443 
[1] "4p gain"
[1] 3
      4P GAIN CNV 4P GAIN WILD-TYPE 
               30               442 
      4P GAIN CNV 4P GAIN WILD-TYPE 
               30               442 
[1] "4q gain"
[1] 3
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
               11               461 
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
               11               461 
[1] "5p gain"
[1] 3
      5P GAIN CNV 5P GAIN WILD-TYPE 
              178               294 
      5P GAIN CNV 5P GAIN WILD-TYPE 
              178               294 
[1] "5q gain"
[1] 3
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
               56               416 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
               56               416 
[1] "6p gain"
[1] 3
      6P GAIN CNV 6P GAIN WILD-TYPE 
               71               401 
      6P GAIN CNV 6P GAIN WILD-TYPE 
               71               401 
[1] "6q gain"
[1] 3
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
               20               452 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
               20               452 
[1] "7p gain"
[1] 3
      7P GAIN CNV 7P GAIN WILD-TYPE 
              154               318 
      7P GAIN CNV 7P GAIN WILD-TYPE 
              154               318 
[1] "7q gain"
[1] 3
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
              111               361 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
              111               361 
[1] "8p gain"
[1] 3
      8P GAIN CNV 8P GAIN WILD-TYPE 
               59               413 
      8P GAIN CNV 8P GAIN WILD-TYPE 
               59               413 
[1] "8q gain"
[1] 3
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
              144               328 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
              144               328 
[1] "9p gain"
[1] 3
      9P GAIN CNV 9P GAIN WILD-TYPE 
               14               458 
      9P GAIN CNV 9P GAIN WILD-TYPE 
               14               458 
[1] "9q gain"
[1] 3
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                7               465 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                7               465 
[1] "10p gain"
[1] 3
      10P GAIN CNV 10P GAIN WILD-TYPE 
                49                423 
      10P GAIN CNV 10P GAIN WILD-TYPE 
                49                423 
[1] "10q gain"
[1] 3
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                28                444 
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                28                444 
[1] "11p gain"
[1] 3
      11P GAIN CNV 11P GAIN WILD-TYPE 
                35                437 
      11P GAIN CNV 11P GAIN WILD-TYPE 
                35                437 
[1] "11q gain"
[1] 3
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                51                421 
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                51                421 
[1] "12p gain"
[1] 3
      12P GAIN CNV 12P GAIN WILD-TYPE 
                57                415 
      12P GAIN CNV 12P GAIN WILD-TYPE 
                57                415 
[1] "12q gain"
[1] 3
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                46                426 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                46                426 
[1] "13q gain"
[1] 3
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                15                457 
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                15                457 
[1] "14q gain"
[1] 3
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                56                416 
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                56                416 
[1] "15q gain"
[1] 3
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                14                458 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                14                458 
[1] "16p gain"
[1] 3
      16P GAIN CNV 16P GAIN WILD-TYPE 
                67                405 
      16P GAIN CNV 16P GAIN WILD-TYPE 
                67                405 
[1] "16q gain"
[1] 3
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                42                430 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                42                430 
[1] "17p gain"
[1] 3
      17P GAIN CNV 17P GAIN WILD-TYPE 
                28                444 
      17P GAIN CNV 17P GAIN WILD-TYPE 
                28                444 
[1] "17q gain"
[1] 3
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                78                394 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                78                394 
[1] "18p gain"
[1] 3
      18P GAIN CNV 18P GAIN WILD-TYPE 
                42                430 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                42                430 
[1] "18q gain"
[1] 3
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                26                446 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                26                446 
[1] "19p gain"
[1] 3
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 6                466 
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 6                466 
[1] "19q gain"
[1] 3
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                22                450 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                22                450 
[1] "20p gain"
[1] 3
      20P GAIN CNV 20P GAIN WILD-TYPE 
                61                411 
      20P GAIN CNV 20P GAIN WILD-TYPE 
                61                411 
[1] "20q gain"
[1] 3
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                76                396 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                76                396 
[1] "21q gain"
[1] 3
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                41                431 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                41                431 
[1] "22q gain"
[1] 3
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                20                452 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                20                452 
[1] "Xq gain"
[1] 3
      XQ GAIN CNV XQ GAIN WILD-TYPE 
               19               453 
      XQ GAIN CNV XQ GAIN WILD-TYPE 
               19               453 
[1] "1p loss"
[1] 3
      1P LOSS CNV 1P LOSS WILD-TYPE 
               28               444 
      1P LOSS CNV 1P LOSS WILD-TYPE 
               28               444 
[1] "1q loss"
[1] 3
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
               11               461 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
               11               461 
[1] "2p loss"
[1] 3
      2P LOSS CNV 2P LOSS WILD-TYPE 
                6               466 
      2P LOSS CNV 2P LOSS WILD-TYPE 
                6               466 
[1] "2q loss"
[1] 3
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                4               468 
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                4               468 
[1] "3p loss"
[1] 3
      3P LOSS CNV 3P LOSS WILD-TYPE 
               93               379 
      3P LOSS CNV 3P LOSS WILD-TYPE 
               93               379 
[1] "3q loss"
[1] 3
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
               56               416 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
               56               416 
[1] "4p loss"
[1] 3
      4P LOSS CNV 4P LOSS WILD-TYPE 
               38               434 
      4P LOSS CNV 4P LOSS WILD-TYPE 
               38               434 
[1] "4q loss"
[1] 3
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               45               427 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               45               427 
[1] "5p loss"
[1] 3
      5P LOSS CNV 5P LOSS WILD-TYPE 
               15               457 
      5P LOSS CNV 5P LOSS WILD-TYPE 
               15               457 
[1] "5q loss"
[1] 3
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
               58               414 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
               58               414 
[1] "6p loss"
[1] 3
      6P LOSS CNV 6P LOSS WILD-TYPE 
               38               434 
      6P LOSS CNV 6P LOSS WILD-TYPE 
               38               434 
[1] "6q loss"
[1] 3
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
              105               367 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
              105               367 
[1] "7p loss"
[1] 3
      7P LOSS CNV 7P LOSS WILD-TYPE 
               14               458 
      7P LOSS CNV 7P LOSS WILD-TYPE 
               14               458 
[1] "7q loss"
[1] 3
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
               17               455 
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
               17               455 
[1] "8p loss"
[1] 3
      8P LOSS CNV 8P LOSS WILD-TYPE 
              118               354 
      8P LOSS CNV 8P LOSS WILD-TYPE 
              118               354 
[1] "8q loss"
[1] 3
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
               17               455 
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
               17               455 
[1] "9p loss"
[1] 3
      9P LOSS CNV 9P LOSS WILD-TYPE 
              139               333 
      9P LOSS CNV 9P LOSS WILD-TYPE 
              139               333 
[1] "9q loss"
[1] 3
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
              117               355 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
              117               355 
[1] "10p loss"
[1] 3
      10P LOSS CNV 10P LOSS WILD-TYPE 
                35                437 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                35                437 
[1] "10q loss"
[1] 3
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                45                427 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                45                427 
[1] "11p loss"
[1] 3
      11P LOSS CNV 11P LOSS WILD-TYPE 
                32                440 
      11P LOSS CNV 11P LOSS WILD-TYPE 
                32                440 
[1] "11q loss"
[1] 3
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                29                443 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                29                443 
[1] "12p loss"
[1] 3
      12P LOSS CNV 12P LOSS WILD-TYPE 
                37                435 
      12P LOSS CNV 12P LOSS WILD-TYPE 
                37                435 
[1] "12q loss"
[1] 3
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                23                449 
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                23                449 
[1] "13q loss"
[1] 3
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
               109                363 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
               109                363 
[1] "14q loss"
[1] 3
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                46                426 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                46                426 
[1] "15q loss"
[1] 3
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                95                377 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                95                377 
[1] "16p loss"
[1] 3
      16P LOSS CNV 16P LOSS WILD-TYPE 
                37                435 
      16P LOSS CNV 16P LOSS WILD-TYPE 
                37                435 
[1] "16q loss"
[1] 3
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                56                416 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                56                416 
[1] "17p loss"
[1] 3
      17P LOSS CNV 17P LOSS WILD-TYPE 
               109                363 
      17P LOSS CNV 17P LOSS WILD-TYPE 
               109                363 
[1] "17q loss"
[1] 3
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                17                455 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                17                455 
[1] "18p loss"
[1] 3
      18P LOSS CNV 18P LOSS WILD-TYPE 
                75                397 
      18P LOSS CNV 18P LOSS WILD-TYPE 
                75                397 
[1] "18q loss"
[1] 3
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
               108                364 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
               108                364 
[1] "19p loss"
[1] 3
      19P LOSS CNV 19P LOSS WILD-TYPE 
               112                360 
      19P LOSS CNV 19P LOSS WILD-TYPE 
               112                360 
[1] "19q loss"
[1] 3
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                67                405 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                67                405 
[1] "20p loss"
[1] 3
      20P LOSS CNV 20P LOSS WILD-TYPE 
                61                411 
      20P LOSS CNV 20P LOSS WILD-TYPE 
                61                411 
[1] "20q loss"
[1] 3
      20Q LOSS CNV 20Q LOSS WILD-TYPE 
                24                448 
      20Q LOSS CNV 20Q LOSS WILD-TYPE 
                24                448 
[1] "21q loss"
[1] 3
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                66                406 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                66                406 
[1] "22q loss"
[1] 3
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                90                382 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                90                382 
[1] "Xq loss"
[1] 3
      XQ LOSS CNV XQ LOSS WILD-TYPE 
               11               461 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
               11               461 
[1] "data2feature, selection="
 [1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
 [4] "METHLYATION_CNMF"      "RPPA_CNMF"             "RPPA_CHIERARCHICAL"   
 [7] "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"          
[10] "MIRSEQ_CHIERARCHICAL" 

Input Data has 10 rows and 472 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
 [4] "METHLYATION_CNMF"      "RPPA_CNMF"             "RPPA_CHIERARCHICAL"   
 [7] "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"          
[10] "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 472 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
CN_CNMF, nv=4, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=5, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=9, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain
D1V1, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           0                 5
  CLUS_2           1                 8
  CLUS_3           2                10
  CLUS_4           1                 5
D1V2, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           1                 6
  CLUS_2           2                11
  CLUS_3           1                11
D1V3, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1          39               109
  CLUS_2           9               179
  CLUS_3           6                81
  CLUS_4           4                45
D1V4, multiclass
D1V5, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1          14                71
  CLUS_2           4                71
  CLUS_3           8                67
D1V6, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           1                22
  CLUS_2          17                72
  CLUS_3           3                62
  CLUS_4           5                53
D1V7, multiclass
D1V8, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1          18               140
  CLUS_2          18                87
  CLUS_3          14               114
D1V9, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1          18               153
  CLUS_2          25               173
  CLUS_3          14                84
D1V10, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1          19               145
  CLUS_2          29               215
  CLUS_3           9                50

Clustering(2) Variable = 1q gain
D2V1, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           0                 5
  CLUS_2           3                 6
  CLUS_3           5                 7
  CLUS_4           2                 4
D2V2, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           2                 5
  CLUS_2           5                 8
  CLUS_3           3                 9
D2V3, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          67                81
  CLUS_2          59               129
  CLUS_3          29                58
  CLUS_4          22                27
D2V4, multiclass
D2V5, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          30                55
  CLUS_2          33                42
  CLUS_3          21                54
D2V6, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           5                18
  CLUS_2          34                55
  CLUS_3          19                46
  CLUS_4          26                32
D2V7, multiclass
D2V8, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          65                93
  CLUS_2          39                66
  CLUS_3          47                81
D2V9, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          64               107
  CLUS_2          78               120
  CLUS_3          32                66
D2V10, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          65                99
  CLUS_2          90               154
  CLUS_3          19                40

Clustering(3) Variable = 2p gain
D3V1, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           2                 3
  CLUS_2           0                 9
  CLUS_3           1                11
  CLUS_4           3                 3
D3V2, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           4                 3
  CLUS_2           1                12
  CLUS_3           1                11
D3V3, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1          21               127
  CLUS_2           3               185
  CLUS_3          15                72
  CLUS_4          11                38
D3V4, multiclass
D3V5, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           7                78
  CLUS_2           8                67
  CLUS_3          15                60
D3V6, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           1                22
  CLUS_2           7                82
  CLUS_3          15                50
  CLUS_4           7                51
D3V7, multiclass
D3V8, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1          11               147
  CLUS_2           8                97
  CLUS_3          26               102
D3V9, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1          10               161
  CLUS_2          35               163
  CLUS_3           5                93
D3V10, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1          10               154
  CLUS_2          37               207
  CLUS_3           3                56

Clustering(4) Variable = 2q gain
D4V1, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           0                 5
  CLUS_2           0                 9
  CLUS_3           1                11
  CLUS_4           3                 3
D4V2, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           3                 4
  CLUS_2           1                12
  CLUS_3           0                12
D4V3, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1          13               135
  CLUS_2           5               183
  CLUS_3          15                72
  CLUS_4          12                37
D4V4, multiclass
D4V5, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           5                80
  CLUS_2           9                66
  CLUS_3          10                65
D4V6, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           1                22
  CLUS_2           6                83
  CLUS_3          10                55
  CLUS_4           7                51
D4V7, multiclass
D4V8, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1          13               145
  CLUS_2           6                99
  CLUS_3          21               107
D4V9, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1          10               161
  CLUS_2          32               166
  CLUS_3           3                95
D4V10, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1          10               154
  CLUS_2          34               210
  CLUS_3           1                58

Clustering(5) Variable = 3p gain
D5V1, multiclass
D5V2, multiclass
D5V3, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           6               142
  CLUS_2           1               187
  CLUS_3           5                82
  CLUS_4           1                48
D5V4, multiclass
D5V5, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           4                81
  CLUS_2           0                75
  CLUS_3           4                71
D5V6, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           0                23
  CLUS_2           2                87
  CLUS_3           5                60
  CLUS_4           1                57
D5V7, multiclass
D5V8, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           0               158
  CLUS_2           7                98
  CLUS_3           5               123
D5V9, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           4               167
  CLUS_2           6               192
  CLUS_3           3                95
D5V10, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           3               161
  CLUS_2           8               236
  CLUS_3           2                57

Clustering(6) Variable = 3q gain
D6V1, multiclass
[1] "Remove cluster labels:" "3Q GAIN CNV"           
clus
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-55-1595        TCGA-55-1596        TCGA-64-1676        TCGA-64-1677 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
D6V2, multiclass
[1] "Remove cluster labels:" "3Q GAIN CNV"           
clus
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-55-1595        TCGA-55-1596        TCGA-64-1676        TCGA-64-1677 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
D6V3, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1          10               138
  CLUS_2           4               184
  CLUS_3          12                75
  CLUS_4           3                46
D6V4, multiclass
D6V5, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           5                80
  CLUS_2           2                73
  CLUS_3           9                66
D6V6, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           0                23
  CLUS_2           3                86
  CLUS_3          10                55
  CLUS_4           3                55
D6V7, multiclass
D6V8, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           5               153
  CLUS_2           8                97
  CLUS_3          11               117
D6V9, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           7               164
  CLUS_2          19               179
  CLUS_3           3                95
D6V10, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           7               157
  CLUS_2          19               225
  CLUS_3           3                56

Clustering(7) Variable = 4p gain
D7V1, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           0                 5
  CLUS_2           0                 9
  CLUS_3           2                10
  CLUS_4           1                 5
D7V2, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           1                 6
  CLUS_2           2                11
  CLUS_3           0                12
D7V3, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1          14               134
  CLUS_2           4               184
  CLUS_3          10                77
  CLUS_4           2                47
D7V4, multiclass
D7V5, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           7                78
  CLUS_2           2                73
  CLUS_3           9                66
D7V6, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           0                23
  CLUS_2           8                81
  CLUS_3           9                56
  CLUS_4           1                57
D7V7, multiclass
D7V8, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           7               151
  CLUS_2           9                96
  CLUS_3          10               118
D7V9, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           8               163
  CLUS_2          15               183
  CLUS_3           7                91
D7V10, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           7               157
  CLUS_2          19               225
  CLUS_3           4                55

Clustering(8) Variable = 4q gain
D8V1, multiclass
[1] "Remove cluster labels:" "4Q GAIN CNV"           
clus
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1595        TCGA-55-1596        TCGA-64-1676 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-64-1677        TCGA-64-1678        TCGA-67-3770        TCGA-67-3771 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V2, multiclass
[1] "Remove cluster labels:" "4Q GAIN CNV"           
clus
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1595        TCGA-55-1596        TCGA-64-1676 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-64-1677        TCGA-64-1678        TCGA-67-3770        TCGA-67-3771 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V3, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           7               141
  CLUS_2           1               187
  CLUS_3           3                84
  CLUS_4           0                49
D8V4, multiclass
D8V5, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           2                83
  CLUS_2           1                74
  CLUS_3           5                70
D8V6, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           0                23
  CLUS_2           2                87
  CLUS_3           5                60
  CLUS_4           1                57
D8V7, multiclass
D8V8, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           2               156
  CLUS_2           5               100
  CLUS_3           3               125
D8V9, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           1               170
  CLUS_2           6               192
  CLUS_3           4                94
D8V10, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           1               163
  CLUS_2           8               236
  CLUS_3           2                57

Clustering(9) Variable = 5p gain
D9V1, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           3                 2
  CLUS_2           2                 7
  CLUS_3           6                 6
  CLUS_4           2                 4
D9V2, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           3                 4
  CLUS_2           7                 6
  CLUS_3           3                 9
D9V3, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          93                55
  CLUS_2          39               149
  CLUS_3          24                63
  CLUS_4          22                27
D9V4, multiclass
D9V5, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          37                48
  CLUS_2          30                45
  CLUS_3          23                52
D9V6, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           6                17
  CLUS_2          35                54
  CLUS_3          27                38
  CLUS_4          22                36
D9V7, multiclass
D9V8, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          50               108
  CLUS_2          50                55
  CLUS_3          46                82
D9V9, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          57               114
  CLUS_2          84               114
  CLUS_3          35                63
D9V10, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          52               112
  CLUS_2          97               147
  CLUS_3          27                32

Clustering(10) Variable = 5q gain
D10V1, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           3                 2
  CLUS_2           0                 9
  CLUS_3           4                 8
  CLUS_4           0                 6
D10V2, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           1                 6
  CLUS_2           4                 9
  CLUS_3           2                10
D10V3, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          25               123
  CLUS_2          17               171
  CLUS_3           6                81
  CLUS_4           8                41
D10V4, multiclass
D10V5, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          11                74
  CLUS_2          10                65
  CLUS_3           6                69
D10V6, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           0                23
  CLUS_2          12                77
  CLUS_3           6                59
  CLUS_4           9                49
D10V7, multiclass
D10V8, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          25               133
  CLUS_2          11                94
  CLUS_3           8               120
D10V9, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          23               148
  CLUS_2          19               179
  CLUS_3          14                84
D10V10, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          25               139
  CLUS_2          22               222
  CLUS_3           9                50

Clustering(11) Variable = 6p gain
D11V1, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           1                 4
  CLUS_2           0                 9
  CLUS_3           3                 9
  CLUS_4           2                 4
D11V2, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           3                 4
  CLUS_2           3                10
  CLUS_3           0                12
D11V3, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1          29               119
  CLUS_2          19               169
  CLUS_3          11                76
  CLUS_4          12                37
D11V4, multiclass
D11V5, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           6                79
  CLUS_2          18                57
  CLUS_3          10                65
D11V6, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           2                21
  CLUS_2           9                80
  CLUS_3          11                54
  CLUS_4          12                46
D11V7, multiclass
D11V8, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1          30               128
  CLUS_2          12                93
  CLUS_3          19               109
D11V9, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1          22               149
  CLUS_2          37               161
  CLUS_3           9                89
D11V10, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1          21               143
  CLUS_2          41               203
  CLUS_3           6                53

Clustering(12) Variable = 6q gain
D12V1, multiclass
D12V2, multiclass
D12V3, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           7               141
  CLUS_2           5               183
  CLUS_3           6                81
  CLUS_4           2                47
D12V4, multiclass
D12V5, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           1                84
  CLUS_2           3                72
  CLUS_3           6                69
D12V6, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           1                22
  CLUS_2           3                86
  CLUS_3           6                59
  CLUS_4           0                58
D12V7, multiclass
D12V8, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           5               153
  CLUS_2           5               100
  CLUS_3           8               120
D12V9, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           3               168
  CLUS_2          13               185
  CLUS_3           4                94
D12V10, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           2               162
  CLUS_2          16               228
  CLUS_3           2                57

Clustering(13) Variable = 7p gain
D13V1, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           1                 4
  CLUS_2           2                 7
  CLUS_3           3                 9
  CLUS_4           0                 6
D13V2, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           0                 7
  CLUS_2           3                10
  CLUS_3           3                 9
D13V3, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          89                59
  CLUS_2          26               162
  CLUS_3          28                59
  CLUS_4          11                38
D13V4, multiclass
D13V5, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          38                47
  CLUS_2          13                62
  CLUS_3          35                40
D13V6, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           5                18
  CLUS_2          41                48
  CLUS_3          27                38
  CLUS_4          13                45
D13V7, multiclass
D13V8, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          39               119
  CLUS_2          58                47
  CLUS_3          36                92
D13V9, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          39               132
  CLUS_2          70               128
  CLUS_3          44                54
D13V10, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          40               124
  CLUS_2          86               158
  CLUS_3          27                32

Clustering(14) Variable = 7q gain
D14V1, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           0                 5
  CLUS_2           3                 6
  CLUS_3           1                11
  CLUS_4           1                 5
D14V2, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           1                 6
  CLUS_2           1                12
  CLUS_3           3                 9
D14V3, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          61                87
  CLUS_2          22               166
  CLUS_3          20                67
  CLUS_4           8                41
D14V4, multiclass
D14V5, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          28                57
  CLUS_2          13                62
  CLUS_3          19                56
D14V6, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           4                19
  CLUS_2          29                60
  CLUS_3          14                51
  CLUS_4          13                45
D14V7, multiclass
D14V8, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          29               129
  CLUS_2          45                60
  CLUS_3          24               104
D14V9, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          32               139
  CLUS_2          49               149
  CLUS_3          28                70
D14V10, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          31               133
  CLUS_2          62               182
  CLUS_3          16                43

Clustering(15) Variable = 8p gain
D15V1, multiclass
[1] "Remove cluster labels:" "8P GAIN CNV"           
clus
      8P GAIN CNV 8P GAIN WILD-TYPE 
                2                30 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1595        TCGA-64-1676        TCGA-64-1677 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-64-1678        TCGA-67-3770        TCGA-67-3771        TCGA-67-3772 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-67-3773        TCGA-67-3774 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
D15V2, multiclass
[1] "Remove cluster labels:" "8P GAIN CNV"           
clus
      8P GAIN CNV 8P GAIN WILD-TYPE 
                2                30 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1595        TCGA-64-1676        TCGA-64-1677 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-64-1678        TCGA-67-3770        TCGA-67-3771        TCGA-67-3772 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-67-3773        TCGA-67-3774 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
D15V3, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          14               134
  CLUS_2          11               177
  CLUS_3          11                76
  CLUS_4          23                26
D15V4, multiclass
D15V5, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          13                72
  CLUS_2           8                67
  CLUS_3          12                63
D15V6, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           2                21
  CLUS_2          12                77
  CLUS_3          11                54
  CLUS_4           8                50
D15V7, multiclass
D15V8, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          17               141
  CLUS_2           5               100
  CLUS_3          23               105
D15V9, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          17               154
  CLUS_2          25               173
  CLUS_3          15                83
D15V10, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          14               150
  CLUS_2          34               210
  CLUS_3           9                50

Clustering(16) Variable = 8q gain
D16V1, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           1                 4
  CLUS_2           3                 6
  CLUS_3           1                11
  CLUS_4           4                 2
D16V2, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           4                 3
  CLUS_2           2                11
  CLUS_3           3                 9
D16V3, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          56                92
  CLUS_2          17               171
  CLUS_3          34                53
  CLUS_4          37                12
D16V4, multiclass
D16V5, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          30                55
  CLUS_2          16                59
  CLUS_3          30                45
D16V6, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           4                19
  CLUS_2          36                53
  CLUS_3          26                39
  CLUS_4          10                48
D16V7, multiclass
D16V8, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          32               126
  CLUS_2          34                71
  CLUS_3          51                77
D16V9, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          27               144
  CLUS_2          81               117
  CLUS_3          34                64
D16V10, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          27               137
  CLUS_2         100               144
  CLUS_3          15                44

Clustering(17) Variable = 9p gain
D17V1, multiclass
D17V2, multiclass
D17V3, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           9               139
  CLUS_2           1               187
  CLUS_3           3                84
  CLUS_4           1                48
D17V4, multiclass
D17V5, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           2                83
  CLUS_2           2                73
  CLUS_3           1                74
D17V6, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           0                23
  CLUS_2           2                87
  CLUS_3           1                64
  CLUS_4           2                56
D17V7, multiclass
D17V8, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           3               155
  CLUS_2           6                99
  CLUS_3           3               125
D17V9, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           3               168
  CLUS_2           8               190
  CLUS_3           3                95
D17V10, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           2               162
  CLUS_2          10               234
  CLUS_3           2                57

Clustering(18) Variable = 9q gain
D18V1, multiclass
D18V2, multiclass
D18V3, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           4               144
  CLUS_2           1               187
  CLUS_3           2                85
  CLUS_4           0                49
D18V4, multiclass
D18V5, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           0                85
  CLUS_2           2                73
  CLUS_3           2                73
D18V6, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           0                23
  CLUS_2           0                89
  CLUS_3           2                63
  CLUS_4           2                56
D18V7, multiclass
D18V8, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           3               155
  CLUS_2           2               103
  CLUS_3           2               126
D18V9, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           1               170
  CLUS_2           3               195
  CLUS_3           3                95
D18V10, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           1               163
  CLUS_2           4               240
  CLUS_3           2                57

Clustering(19) Variable = 10p gain
D19V1, multiclass
[1] "Remove cluster labels:" "10P GAIN CNV"          
clus
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1680         TCGA-67-3770 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-67-3774 
"10P GAIN WILD-TYPE" 
D19V2, multiclass
[1] "Remove cluster labels:" "10P GAIN CNV"          
clus
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1680         TCGA-67-3770 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-67-3774 
"10P GAIN WILD-TYPE" 
D19V3, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           19                129
  CLUS_2           11                177
  CLUS_3           11                 76
  CLUS_4            8                 41
D19V4, multiclass
D19V5, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            6                 79
  CLUS_2           11                 64
  CLUS_3           12                 63
D19V6, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            4                 19
  CLUS_2            6                 83
  CLUS_3           11                 54
  CLUS_4            8                 50
D19V7, multiclass
D19V8, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           12                146
  CLUS_2           11                 94
  CLUS_3           20                108
D19V9, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           16                155
  CLUS_2           26                172
  CLUS_3            5                 93
D19V10, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           15                149
  CLUS_2           29                215
  CLUS_3            3                 56

Clustering(20) Variable = 10q gain
D20V1, multiclass
D20V2, multiclass
D20V3, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            7                141
  CLUS_2            9                179
  CLUS_3            5                 82
  CLUS_4            7                 42
D20V4, multiclass
D20V5, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            4                 81
  CLUS_2            7                 68
  CLUS_3            5                 70
D20V6, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            2                 21
  CLUS_2            3                 86
  CLUS_3            4                 61
  CLUS_4            7                 51
D20V7, multiclass
D20V8, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1           11                147
  CLUS_2            3                102
  CLUS_3           10                118
D20V9, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1           12                159
  CLUS_2           10                188
  CLUS_3            4                 94
D20V10, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1           12                152
  CLUS_2           13                231
  CLUS_3            1                 58

Clustering(21) Variable = 11p gain
D21V1, multiclass
[1] "Remove cluster labels:" "11P GAIN CNV"          
clus
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1595 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-67-3774 
"11P GAIN WILD-TYPE" 
D21V2, multiclass
[1] "Remove cluster labels:" "11P GAIN CNV"          
clus
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1595 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-67-3774 
"11P GAIN WILD-TYPE" 
D21V3, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1           13                135
  CLUS_2            7                181
  CLUS_3           10                 77
  CLUS_4            5                 44
D21V4, multiclass
D21V5, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            5                 80
  CLUS_2            3                 72
  CLUS_3           10                 65
D21V6, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            0                 23
  CLUS_2            7                 82
  CLUS_3            7                 58
  CLUS_4            4                 54
D21V7, multiclass
D21V8, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            9                149
  CLUS_2            8                 97
  CLUS_3           14                114
D21V9, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            6                165
  CLUS_2           19                179
  CLUS_3           10                 88
D21V10, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            7                157
  CLUS_2           23                221
  CLUS_3            5                 54

Clustering(22) Variable = 11q gain
D22V1, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            0                  5
  CLUS_2            1                  8
  CLUS_3            0                 12
  CLUS_4            2                  4
D22V2, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            2                  5
  CLUS_2            1                 12
  CLUS_3            0                 12
D22V3, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1           23                125
  CLUS_2            8                180
  CLUS_3           14                 73
  CLUS_4            6                 43
D22V4, multiclass
D22V5, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            8                 77
  CLUS_2            3                 72
  CLUS_3           18                 57
D22V6, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            0                 23
  CLUS_2           11                 78
  CLUS_3           14                 51
  CLUS_4            4                 54
D22V7, multiclass
D22V8, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            8                150
  CLUS_2           17                 88
  CLUS_3           21                107
D22V9, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            8                163
  CLUS_2           29                169
  CLUS_3           13                 85
D22V10, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            9                155
  CLUS_2           34                210
  CLUS_3            7                 52

Clustering(23) Variable = 12p gain
D23V1, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            1                  4
  CLUS_2            1                  8
  CLUS_3            1                 11
  CLUS_4            2                  4
D23V2, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            3                  4
  CLUS_2            1                 12
  CLUS_3            1                 11
D23V3, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           16                132
  CLUS_2            3                185
  CLUS_3           32                 55
  CLUS_4            6                 43
D23V4, multiclass
D23V5, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           12                 73
  CLUS_2            5                 70
  CLUS_3           12                 63
D23V6, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            0                 23
  CLUS_2           11                 78
  CLUS_3           12                 53
  CLUS_4            6                 52
D23V7, multiclass
D23V8, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            9                149
  CLUS_2           12                 93
  CLUS_3           27                101
D23V9, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            9                162
  CLUS_2           37                161
  CLUS_3           10                 88
D23V10, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           12                152
  CLUS_2           41                203
  CLUS_3            3                 56

Clustering(24) Variable = 12q gain
D24V1, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            1                  4
  CLUS_2            1                  8
  CLUS_3            1                 11
  CLUS_4            2                  4
D24V2, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            3                  4
  CLUS_2            1                 12
  CLUS_3            1                 11
D24V3, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            9                139
  CLUS_2            3                185
  CLUS_3           27                 60
  CLUS_4            7                 42
D24V4, multiclass
D24V5, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            8                 77
  CLUS_2            4                 71
  CLUS_3           11                 64
D24V6, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            0                 23
  CLUS_2            8                 81
  CLUS_3           11                 54
  CLUS_4            4                 54
D24V7, multiclass
D24V8, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            8                150
  CLUS_2            8                 97
  CLUS_3           23                105
D24V9, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            9                162
  CLUS_2           29                169
  CLUS_3            7                 91
D24V10, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1           10                154
  CLUS_2           31                213
  CLUS_3            4                 55

Clustering(25) Variable = 13q gain
D25V1, multiclass
[1] "Remove cluster labels:" "13Q GAIN CNV"          
clus
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1678         TCGA-67-3770 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-67-3772         TCGA-67-3773         TCGA-67-3774 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D25V2, multiclass
[1] "Remove cluster labels:" "13Q GAIN CNV"          
clus
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1678         TCGA-67-3770 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-67-3772         TCGA-67-3773         TCGA-67-3774 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D25V3, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            3                145
  CLUS_2            5                183
  CLUS_3            6                 81
  CLUS_4            1                 48
D25V4, multiclass
D25V5, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            2                 83
  CLUS_2            3                 72
  CLUS_3            5                 70
D25V6, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            0                 23
  CLUS_2            2                 87
  CLUS_3            5                 60
  CLUS_4            3                 55
D25V7, multiclass
D25V8, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            6                152
  CLUS_2            1                104
  CLUS_3            7                121
D25V9, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            5                166
  CLUS_2            7                191
  CLUS_3            2                 96
D25V10, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            4                160
  CLUS_2           10                234
  CLUS_3            0                 59

Clustering(26) Variable = 14q gain
D26V1, multiclass
[1] "Remove cluster labels:" "14Q GAIN CNV"          
clus
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-44-2661         TCGA-44-2662         TCGA-44-2665 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-44-2666         TCGA-44-2668         TCGA-44-3398 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-44-3918         TCGA-44-3919         TCGA-44-4112 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-55-1592         TCGA-55-1594         TCGA-55-1595 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"14Q GAIN WILD-TYPE" 
D26V2, multiclass
[1] "Remove cluster labels:" "14Q GAIN CNV"          
clus
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-44-2661         TCGA-44-2662         TCGA-44-2665 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-44-2666         TCGA-44-2668         TCGA-44-3398 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-44-3918         TCGA-44-3919         TCGA-44-4112 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-55-1592         TCGA-55-1594         TCGA-55-1595 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"14Q GAIN WILD-TYPE" 
D26V3, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1           19                129
  CLUS_2            9                179
  CLUS_3           12                 75
  CLUS_4           16                 33
D26V4, multiclass
D26V5, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            8                 77
  CLUS_2            8                 67
  CLUS_3           15                 60
D26V6, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            2                 21
  CLUS_2           13                 76
  CLUS_3           11                 54
  CLUS_4            5                 53
D26V7, multiclass
D26V8, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1           14                144
  CLUS_2           10                 95
  CLUS_3           25                103
D26V9, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1           10                161
  CLUS_2           30                168
  CLUS_3           15                 83
D26V10, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            7                157
  CLUS_2           38                206
  CLUS_3           10                 49

Clustering(27) Variable = 15q gain
D27V1, multiclass
[1] "Remove cluster labels:" "15Q GAIN CNV"          
clus
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1595 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"15Q GAIN WILD-TYPE" 
D27V2, multiclass
[1] "Remove cluster labels:" "15Q GAIN CNV"          
clus
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1595 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"15Q GAIN WILD-TYPE" 
D27V3, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            5                143
  CLUS_2            3                185
  CLUS_3            5                 82
  CLUS_4            1                 48
D27V4, multiclass
D27V5, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            2                 83
  CLUS_2            3                 72
  CLUS_3            3                 72
D27V6, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            0                 23
  CLUS_2            4                 85
  CLUS_3            1                 64
  CLUS_4            3                 55
D27V7, multiclass
D27V8, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            7                151
  CLUS_2            1                104
  CLUS_3            6                122
D27V9, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            6                165
  CLUS_2            6                192
  CLUS_3            1                 97
D27V10, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            7                157
  CLUS_2            5                239
  CLUS_3            1                 58

Clustering(28) Variable = 16p gain
D28V1, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            2                  3
  CLUS_2            1                  8
  CLUS_3            2                 10
  CLUS_4            0                  6
D28V2, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            0                  7
  CLUS_2            2                 11
  CLUS_3            3                  9
D28V3, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           27                121
  CLUS_2           22                166
  CLUS_3           13                 74
  CLUS_4            5                 44
D28V4, multiclass
D28V5, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           17                 68
  CLUS_2            6                 69
  CLUS_3            9                 66
D28V6, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            3                 20
  CLUS_2           16                 73
  CLUS_3            8                 57
  CLUS_4            5                 53
D28V7, multiclass
D28V8, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           31                127
  CLUS_2           16                 89
  CLUS_3           10                118
D28V9, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           25                146
  CLUS_2           22                176
  CLUS_3           19                 79
D28V10, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           27                137
  CLUS_2           27                217
  CLUS_3           12                 47

Clustering(29) Variable = 16q gain
D29V1, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            1                  4
  CLUS_2            2                  7
  CLUS_3            0                 12
  CLUS_4            0                  6
D29V2, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            0                  7
  CLUS_2            0                 13
  CLUS_3            3                  9
D29V3, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           17                131
  CLUS_2           13                175
  CLUS_3            9                 78
  CLUS_4            3                 46
D29V4, multiclass
D29V5, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           12                 73
  CLUS_2            2                 73
  CLUS_3            9                 66
D29V6, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            1                 22
  CLUS_2           14                 75
  CLUS_3            7                 58
  CLUS_4            1                 57
D29V7, multiclass
D29V8, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           19                139
  CLUS_2           12                 93
  CLUS_3            8                120
D29V9, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           15                156
  CLUS_2           13                185
  CLUS_3           13                 85
D29V10, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           14                150
  CLUS_2           17                227
  CLUS_3           10                 49

Clustering(30) Variable = 17p gain
D30V1, multiclass
[1] "Remove cluster labels:" "17P GAIN CNV"          
clus
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1678         TCGA-67-3770 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-67-3774 
"17P GAIN WILD-TYPE" 
D30V2, multiclass
[1] "Remove cluster labels:" "17P GAIN CNV"          
clus
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1678         TCGA-67-3770 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-67-3774 
"17P GAIN WILD-TYPE" 
D30V3, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            5                143
  CLUS_2            3                185
  CLUS_3           13                 74
  CLUS_4            7                 42
D30V4, multiclass
D30V5, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            5                 80
  CLUS_2            2                 73
  CLUS_3            3                 72
D30V6, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            1                 22
  CLUS_2            2                 87
  CLUS_3            3                 62
  CLUS_4            4                 54
D30V7, multiclass
D30V8, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            8                150
  CLUS_2            6                 99
  CLUS_3           12                116
D30V9, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            8                163
  CLUS_2           17                181
  CLUS_3            2                 96
D30V10, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            7                157
  CLUS_2           19                225
  CLUS_3            1                 58

Clustering(31) Variable = 17q gain
D31V1, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            3                  2
  CLUS_2            1                  8
  CLUS_3            1                 11
  CLUS_4            0                  6
D31V2, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            1                  6
  CLUS_2            1                 12
  CLUS_3            3                  9
D31V3, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           37                111
  CLUS_2            9                179
  CLUS_3           22                 65
  CLUS_4           10                 39
D31V4, multiclass
D31V5, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           15                 70
  CLUS_2            8                 67
  CLUS_3           13                 62
D31V6, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            1                 22
  CLUS_2           16                 73
  CLUS_3           13                 52
  CLUS_4            6                 52
D31V7, multiclass
D31V8, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           22                136
  CLUS_2           26                 79
  CLUS_3           19                109
D31V9, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           19                152
  CLUS_2           43                155
  CLUS_3           15                 83
D31V10, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           19                145
  CLUS_2           51                193
  CLUS_3            7                 52

Clustering(32) Variable = 18p gain
D32V1, multiclass
D32V2, multiclass
D32V3, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1           22                126
  CLUS_2            5                183
  CLUS_3            4                 83
  CLUS_4           11                 38
D32V4, multiclass
D32V5, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            3                 82
  CLUS_2           10                 65
  CLUS_3            6                 69
D32V6, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            1                 22
  CLUS_2            4                 85
  CLUS_3            6                 59
  CLUS_4            8                 50
D32V7, multiclass
D32V8, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            9                149
  CLUS_2            9                 96
  CLUS_3           18                110
D32V9, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            8                163
  CLUS_2           26                172
  CLUS_3            8                 90
D32V10, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            8                156
  CLUS_2           31                213
  CLUS_3            3                 56

Clustering(33) Variable = 18q gain
D33V1, multiclass
[1] "Remove cluster labels:" "18Q GAIN CNV"          
clus
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1680         TCGA-67-3770 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"18Q GAIN WILD-TYPE" 
D33V2, multiclass
[1] "Remove cluster labels:" "18Q GAIN CNV"          
clus
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1680         TCGA-67-3770 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"18Q GAIN WILD-TYPE" 
D33V3, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1           12                136
  CLUS_2            2                186
  CLUS_3            3                 84
  CLUS_4            9                 40
D33V4, multiclass
D33V5, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            2                 83
  CLUS_2            4                 71
  CLUS_3            8                 67
D33V6, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            1                 22
  CLUS_2            1                 88
  CLUS_3            7                 58
  CLUS_4            5                 53
D33V7, multiclass
D33V8, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            3                155
  CLUS_2            4                101
  CLUS_3           15                113
D33V9, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            5                166
  CLUS_2           16                182
  CLUS_3            5                 93
D33V10, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            4                160
  CLUS_2           20                224
  CLUS_3            2                 57

Clustering(34) Variable = 19p gain
D34V1, multiclass
[1] "Remove cluster labels:" "19P GAIN CNV"          
clus
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2666 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-44-2668         TCGA-44-3398         TCGA-44-3918 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-44-3919         TCGA-44-4112         TCGA-55-1592 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-55-1594         TCGA-55-1595         TCGA-55-1596 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-64-1676         TCGA-64-1677         TCGA-64-1678 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-64-1680         TCGA-67-3770         TCGA-67-3771 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-67-3772         TCGA-67-3773         TCGA-67-3774 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
D34V2, multiclass
[1] "Remove cluster labels:" "19P GAIN CNV"          
clus
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2666 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-44-2668         TCGA-44-3398         TCGA-44-3918 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-44-3919         TCGA-44-4112         TCGA-55-1592 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-55-1594         TCGA-55-1595         TCGA-55-1596 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-64-1676         TCGA-64-1677         TCGA-64-1678 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-64-1680         TCGA-67-3770         TCGA-67-3771 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-67-3772         TCGA-67-3773         TCGA-67-3774 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
D34V3, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            1                147
  CLUS_2            3                185
  CLUS_3            1                 86
  CLUS_4            1                 48
D34V4, multiclass
D34V5, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            2                 83
  CLUS_2            0                 75
  CLUS_3            1                 74
D34V6, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            0                 23
  CLUS_2            1                 88
  CLUS_3            1                 64
  CLUS_4            1                 57
D34V7, multiclass
D34V8, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            2                156
  CLUS_2            2                103
  CLUS_3            2                126
D34V9, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            1                170
  CLUS_2            3                195
  CLUS_3            2                 96
D34V10, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            2                162
  CLUS_2            3                241
  CLUS_3            1                 58

Clustering(35) Variable = 19q gain
D35V1, multiclass
[1] "Remove cluster labels:" "19Q GAIN CNV"          
clus
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2665 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-44-2666         TCGA-44-2668         TCGA-44-3398 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-44-3918         TCGA-44-3919         TCGA-44-4112 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-55-1592         TCGA-55-1594         TCGA-55-1595 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"19Q GAIN WILD-TYPE" 
D35V2, multiclass
[1] "Remove cluster labels:" "19Q GAIN CNV"          
clus
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2665 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-44-2666         TCGA-44-2668         TCGA-44-3398 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-44-3918         TCGA-44-3919         TCGA-44-4112 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-55-1592         TCGA-55-1594         TCGA-55-1595 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"19Q GAIN WILD-TYPE" 
D35V3, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            3                145
  CLUS_2            4                184
  CLUS_3            8                 79
  CLUS_4            7                 42
D35V4, multiclass
D35V5, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            2                 83
  CLUS_2            2                 73
  CLUS_3            5                 70
D35V6, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            2                 21
  CLUS_2            0                 89
  CLUS_3            5                 60
  CLUS_4            2                 56
D35V7, multiclass
D35V8, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            5                153
  CLUS_2            3                102
  CLUS_3           12                116
D35V9, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            4                167
  CLUS_2           14                184
  CLUS_3            4                 94
D35V10, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            4                160
  CLUS_2           17                227
  CLUS_3            1                 58

Clustering(36) Variable = 20p gain
D36V1, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            0                  5
  CLUS_2            1                  8
  CLUS_3            0                 12
  CLUS_4            3                  3
D36V2, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            3                  4
  CLUS_2            0                 13
  CLUS_3            1                 11
D36V3, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           15                133
  CLUS_2           11                177
  CLUS_3           22                 65
  CLUS_4           13                 36
D36V4, multiclass
D36V5, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            9                 76
  CLUS_2            7                 68
  CLUS_3           18                 57
D36V6, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            2                 21
  CLUS_2           13                 76
  CLUS_3           12                 53
  CLUS_4            7                 51
D36V7, multiclass
D36V8, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           15                143
  CLUS_2            8                 97
  CLUS_3           32                 96
D36V9, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           13                158
  CLUS_2           34                164
  CLUS_3           14                 84
D36V10, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           11                153
  CLUS_2           40                204
  CLUS_3           10                 49

Clustering(37) Variable = 20q gain
D37V1, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            0                  5
  CLUS_2            1                  8
  CLUS_3            0                 12
  CLUS_4            4                  2
D37V2, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            4                  3
  CLUS_2            0                 13
  CLUS_3            1                 11
D37V3, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           27                121
  CLUS_2           11                177
  CLUS_3           26                 61
  CLUS_4           12                 37
D37V4, multiclass
D37V5, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           11                 74
  CLUS_2            9                 66
  CLUS_3           25                 50
D37V6, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            3                 20
  CLUS_2           18                 71
  CLUS_3           18                 47
  CLUS_4            6                 52
D37V7, multiclass
D37V8, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           20                138
  CLUS_2           11                 94
  CLUS_3           39                 89
D37V9, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           16                155
  CLUS_2           45                153
  CLUS_3           15                 83
D37V10, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           14                150
  CLUS_2           51                193
  CLUS_3           11                 48

Clustering(38) Variable = 21q gain
D38V1, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            0                  5
  CLUS_2            0                  9
  CLUS_3            1                 11
  CLUS_4            2                  4
D38V2, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            2                  5
  CLUS_2            1                 12
  CLUS_3            0                 12
D38V3, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           27                121
  CLUS_2            8                180
  CLUS_3            4                 83
  CLUS_4            2                 47
D38V4, multiclass
D38V5, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           12                 73
  CLUS_2            3                 72
  CLUS_3            7                 68
D38V6, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            2                 21
  CLUS_2           13                 76
  CLUS_3            6                 59
  CLUS_4            1                 57
D38V7, multiclass
D38V8, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           15                143
  CLUS_2           13                 92
  CLUS_3            7                121
D38V9, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            9                162
  CLUS_2           24                174
  CLUS_3            7                 91
D38V10, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           10                154
  CLUS_2           24                220
  CLUS_3            6                 53

Clustering(39) Variable = 22q gain
D39V1, multiclass
[1] "Remove cluster labels:" "22Q GAIN CNV"          
clus
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1594         TCGA-55-1595 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"22Q GAIN WILD-TYPE" 
D39V2, multiclass
[1] "Remove cluster labels:" "22Q GAIN CNV"          
clus
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1594         TCGA-55-1595 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"22Q GAIN WILD-TYPE" 
D39V3, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            8                140
  CLUS_2            3                185
  CLUS_3            5                 82
  CLUS_4            4                 45
D39V4, multiclass
D39V5, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            4                 81
  CLUS_2            2                 73
  CLUS_3            4                 71
D39V6, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            2                 21
  CLUS_2            2                 87
  CLUS_3            5                 60
  CLUS_4            1                 57
D39V7, multiclass
D39V8, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            5                153
  CLUS_2            6                 99
  CLUS_3            8                120
D39V9, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            3                168
  CLUS_2           11                187
  CLUS_3            6                 92
D39V10, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            3                161
  CLUS_2           12                232
  CLUS_3            5                 54

Clustering(40) Variable = Xq gain
D40V1, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           1                 4
  CLUS_2           1                 8
  CLUS_3           1                11
  CLUS_4           0                 6
D40V2, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           0                 7
  CLUS_2           1                12
  CLUS_3           2                10
D40V3, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1          10               138
  CLUS_2           0               188
  CLUS_3           6                81
  CLUS_4           3                46
D40V4, multiclass
D40V5, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           2                83
  CLUS_2           3                72
  CLUS_3           5                70
D40V6, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           0                23
  CLUS_2           6                83
  CLUS_3           2                63
  CLUS_4           2                56
D40V7, multiclass
D40V8, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           5               153
  CLUS_2           7                98
  CLUS_3           6               122
D40V9, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           5               166
  CLUS_2           9               189
  CLUS_3           5                93
D40V10, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           5               159
  CLUS_2          11               233
  CLUS_3           3                56

Clustering(41) Variable = 1p loss
D41V1, multiclass
[1] "Remove cluster labels:" "1P LOSS CNV"           
clus
      1P LOSS CNV 1P LOSS WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-35-3615        TCGA-35-4122 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-35-4123        TCGA-44-2655        TCGA-44-2656        TCGA-44-2657 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-44-2659        TCGA-44-2661        TCGA-44-2662        TCGA-44-2665 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-44-2666        TCGA-44-2668        TCGA-44-3398        TCGA-44-3918 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-44-3919        TCGA-44-4112        TCGA-55-1592        TCGA-55-1594 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-55-1595        TCGA-55-1596        TCGA-64-1676        TCGA-64-1677 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D41V2, multiclass
[1] "Remove cluster labels:" "1P LOSS CNV"           
clus
      1P LOSS CNV 1P LOSS WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-35-3615        TCGA-35-4122 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-35-4123        TCGA-44-2655        TCGA-44-2656        TCGA-44-2657 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-44-2659        TCGA-44-2661        TCGA-44-2662        TCGA-44-2665 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-44-2666        TCGA-44-2668        TCGA-44-3398        TCGA-44-3918 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-44-3919        TCGA-44-4112        TCGA-55-1592        TCGA-55-1594 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-55-1595        TCGA-55-1596        TCGA-64-1676        TCGA-64-1677 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D41V3, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           5               143
  CLUS_2           7               181
  CLUS_3           8                79
  CLUS_4           8                41
D41V4, multiclass
D41V5, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           4                81
  CLUS_2           4                71
  CLUS_3          10                65
D41V6, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           1                22
  CLUS_2           4                85
  CLUS_3           9                56
  CLUS_4           4                54
D41V7, multiclass
D41V8, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           8               150
  CLUS_2           5               100
  CLUS_3          13               115
D41V9, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1          11               160
  CLUS_2          12               186
  CLUS_3           4                94
D41V10, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           7               157
  CLUS_2          19               225
  CLUS_3           1                58

Clustering(42) Variable = 1q loss
D42V1, multiclass
D42V2, multiclass
D42V3, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           2               146
  CLUS_2           2               186
  CLUS_3           4                83
  CLUS_4           3                46
D42V4, multiclass
D42V5, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           2                83
  CLUS_2           1                74
  CLUS_3           5                70
D42V6, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           1                22
  CLUS_2           1                88
  CLUS_3           6                59
  CLUS_4           0                58
D42V7, multiclass
D42V8, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           3               155
  CLUS_2           2               103
  CLUS_3           6               122
D42V9, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           2               169
  CLUS_2           6               192
  CLUS_3           3                95
D42V10, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           1               163
  CLUS_2           9               235
  CLUS_3           1                58

Clustering(43) Variable = 2p loss
D43V1, multiclass
[1] "Remove cluster labels:" "2P LOSS CNV"           
clus
      2P LOSS CNV 2P LOSS WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-44-2666        TCGA-44-2668        TCGA-44-3398        TCGA-44-3918 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-44-3919        TCGA-44-4112        TCGA-55-1592        TCGA-55-1594 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-55-1595        TCGA-55-1596        TCGA-64-1676        TCGA-64-1677 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D43V2, multiclass
[1] "Remove cluster labels:" "2P LOSS CNV"           
clus
      2P LOSS CNV 2P LOSS WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-44-2666        TCGA-44-2668        TCGA-44-3398        TCGA-44-3918 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-44-3919        TCGA-44-4112        TCGA-55-1592        TCGA-55-1594 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-55-1595        TCGA-55-1596        TCGA-64-1676        TCGA-64-1677 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D43V3, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           2               146
  CLUS_2           2               186
  CLUS_3           1                86
  CLUS_4           1                48
D43V4, multiclass
D43V5, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           1                84
  CLUS_2           1                74
  CLUS_3           1                74
D43V6, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           0                23
  CLUS_2           1                88
  CLUS_3           2                63
  CLUS_4           0                58
D43V7, multiclass
D43V8, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           2               156
  CLUS_2           1               104
  CLUS_3           2               126
D43V9, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           2               169
  CLUS_2           2               196
  CLUS_3           2                96
D43V10, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           2               162
  CLUS_2           3               241
  CLUS_3           1                58

Clustering(44) Variable = 2q loss
D44V1, multiclass
D44V2, multiclass
D44V3, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           2               146
  CLUS_2           0               188
  CLUS_3           2                85
  CLUS_4           0                49
D44V4, multiclass
D44V5, multiclass
[1] "Remove cluster labels:" "2Q LOSS CNV"           
clus
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                2               233 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-05-4384 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4396        TCGA-05-4397        TCGA-05-4398        TCGA-05-4402 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4405        TCGA-05-4410        TCGA-05-4417        TCGA-05-4418 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4420        TCGA-05-4422        TCGA-05-4426        TCGA-05-4427 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4430        TCGA-05-4434        TCGA-05-5420        TCGA-05-5423 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-5425        TCGA-05-5429        TCGA-05-5715        TCGA-35-3615 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-38-4625 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-38-4626        TCGA-38-4627        TCGA-38-4629        TCGA-38-6178 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-2656        TCGA-44-2657        TCGA-44-2661        TCGA-44-2665 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-2668        TCGA-44-3396        TCGA-44-3398        TCGA-44-3918 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-3919        TCGA-44-4112        TCGA-44-5643        TCGA-44-5644 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-5645        TCGA-44-6144        TCGA-44-6145        TCGA-44-6146 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-6147        TCGA-44-6148        TCGA-44-6774        TCGA-44-6775 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-6776        TCGA-44-6777        TCGA-44-6778        TCGA-44-6779 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-7659        TCGA-44-7660        TCGA-44-7661        TCGA-44-7662 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-7667        TCGA-44-7669        TCGA-44-7670        TCGA-44-7671 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-7672        TCGA-49-4486        TCGA-49-4487        TCGA-49-4488 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-4494        TCGA-49-4501        TCGA-49-4505        TCGA-49-4506 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-4507        TCGA-49-4510        TCGA-49-4512        TCGA-49-4514 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-6742        TCGA-49-6743        TCGA-49-6744        TCGA-49-6745 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-6761        TCGA-49-6767        TCGA-50-5044        TCGA-50-5045 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5049        TCGA-50-5051        TCGA-50-5066        TCGA-50-5068 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5072        TCGA-50-5930        TCGA-50-5931        TCGA-50-5932 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5933        TCGA-50-5936        TCGA-50-5939        TCGA-50-5941 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5942        TCGA-50-5944        TCGA-50-5946        TCGA-50-6590 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-6591        TCGA-50-6592        TCGA-50-6593        TCGA-50-6594 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-6595        TCGA-50-6597        TCGA-50-6673        TCGA-50-7109 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-53-7624        TCGA-53-7626        TCGA-53-7813        TCGA-55-1592 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1596        TCGA-55-5899        TCGA-55-6543 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-6712        TCGA-55-6969        TCGA-55-6970        TCGA-55-6971 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-6978        TCGA-55-6979        TCGA-55-6981        TCGA-55-6982 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-7573        TCGA-55-7574        TCGA-55-7728        TCGA-55-7815 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-7910        TCGA-55-7911        TCGA-64-1676        TCGA-64-1677 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1679        TCGA-64-1680        TCGA-64-1681 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-64-5774        TCGA-64-5778        TCGA-64-5779        TCGA-64-5781 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-64-5815        TCGA-67-3771        TCGA-67-6215        TCGA-67-6216 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-67-6217        TCGA-69-7761        TCGA-69-7763        TCGA-69-7764 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-69-7765        TCGA-71-6725        TCGA-73-4658        TCGA-73-4659 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-73-4670        TCGA-73-4675        TCGA-73-4676        TCGA-73-7498 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-73-7499        TCGA-75-5122        TCGA-75-5125        TCGA-75-6203 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-75-6205        TCGA-75-6206        TCGA-75-6207        TCGA-75-6212 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-75-6214        TCGA-75-7027        TCGA-75-7030        TCGA-75-7031 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7143        TCGA-78-7145        TCGA-78-7146        TCGA-78-7147 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7148        TCGA-78-7149        TCGA-78-7150        TCGA-78-7152 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7153        TCGA-78-7154        TCGA-78-7155        TCGA-78-7156 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7158        TCGA-78-7159        TCGA-78-7160        TCGA-78-7161 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7162        TCGA-78-7163        TCGA-78-7166        TCGA-78-7167 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7535        TCGA-78-7536        TCGA-78-7537        TCGA-78-7539 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7540        TCGA-78-7542        TCGA-78-7633        TCGA-80-5607 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-80-5608        TCGA-80-5611        TCGA-83-5908        TCGA-86-6562 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-86-6851        TCGA-86-7701        TCGA-86-7711        TCGA-86-7713 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-86-7953        TCGA-86-7954        TCGA-86-7955        TCGA-91-6828 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-91-6829        TCGA-91-6830        TCGA-91-6831        TCGA-91-6835 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-91-6836        TCGA-91-6840        TCGA-91-6847        TCGA-91-6848 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-91-6849        TCGA-91-7771        TCGA-93-7348        TCGA-95-7039 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-95-7043        TCGA-95-7567        TCGA-95-7944        TCGA-95-7947 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-95-7948        TCGA-97-7546        TCGA-97-7552        TCGA-97-7553 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-97-7554        TCGA-97-7937        TCGA-97-7938        TCGA-97-7941 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-99-7458 
"2Q LOSS WILD-TYPE" 
D44V6, multiclass
[1] "Remove cluster labels:" "2Q LOSS CNV"           
clus
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                2               233 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-05-4384 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4396        TCGA-05-4397        TCGA-05-4398        TCGA-05-4402 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4405        TCGA-05-4410        TCGA-05-4417        TCGA-05-4418 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4420        TCGA-05-4422        TCGA-05-4426        TCGA-05-4427 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4430        TCGA-05-4434        TCGA-05-5420        TCGA-05-5423 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-5425        TCGA-05-5429        TCGA-05-5715        TCGA-35-3615 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-38-4625 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-38-4626        TCGA-38-4627        TCGA-38-4629        TCGA-38-6178 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-2656        TCGA-44-2657        TCGA-44-2661        TCGA-44-2665 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-2668        TCGA-44-3396        TCGA-44-3398        TCGA-44-3918 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-3919        TCGA-44-4112        TCGA-44-5643        TCGA-44-5644 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-5645        TCGA-44-6144        TCGA-44-6145        TCGA-44-6146 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-6147        TCGA-44-6148        TCGA-44-6774        TCGA-44-6775 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-6776        TCGA-44-6777        TCGA-44-6778        TCGA-44-6779 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-7659        TCGA-44-7660        TCGA-44-7661        TCGA-44-7662 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-7667        TCGA-44-7669        TCGA-44-7670        TCGA-44-7671 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-7672        TCGA-49-4486        TCGA-49-4487        TCGA-49-4488 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-4494        TCGA-49-4501        TCGA-49-4505        TCGA-49-4506 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-4507        TCGA-49-4510        TCGA-49-4512        TCGA-49-4514 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-6742        TCGA-49-6743        TCGA-49-6744        TCGA-49-6745 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-6761        TCGA-49-6767        TCGA-50-5044        TCGA-50-5045 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5049        TCGA-50-5051        TCGA-50-5066        TCGA-50-5068 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5072        TCGA-50-5930        TCGA-50-5931        TCGA-50-5932 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5933        TCGA-50-5936        TCGA-50-5939        TCGA-50-5941 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5942        TCGA-50-5944        TCGA-50-5946        TCGA-50-6590 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-6591        TCGA-50-6592        TCGA-50-6593        TCGA-50-6594 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-6595        TCGA-50-6597        TCGA-50-6673        TCGA-50-7109 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-53-7624        TCGA-53-7626        TCGA-53-7813        TCGA-55-1592 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1596        TCGA-55-5899        TCGA-55-6543 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-6712        TCGA-55-6969        TCGA-55-6970        TCGA-55-6971 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-6978        TCGA-55-6979        TCGA-55-6981        TCGA-55-6982 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-7573        TCGA-55-7574        TCGA-55-7728        TCGA-55-7815 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-7910        TCGA-55-7911        TCGA-64-1676        TCGA-64-1677 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1679        TCGA-64-1680        TCGA-64-1681 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-64-5774        TCGA-64-5778        TCGA-64-5779        TCGA-64-5781 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-64-5815        TCGA-67-3771        TCGA-67-6215        TCGA-67-6216 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-67-6217        TCGA-69-7761        TCGA-69-7763        TCGA-69-7764 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-69-7765        TCGA-71-6725        TCGA-73-4658        TCGA-73-4659 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-73-4670        TCGA-73-4675        TCGA-73-4676        TCGA-73-7498 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-73-7499        TCGA-75-5122        TCGA-75-5125        TCGA-75-6203 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-75-6205        TCGA-75-6206        TCGA-75-6207        TCGA-75-6212 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-75-6214        TCGA-75-7027        TCGA-75-7030        TCGA-75-7031 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7143        TCGA-78-7145        TCGA-78-7146        TCGA-78-7147 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7148        TCGA-78-7149        TCGA-78-7150        TCGA-78-7152 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7153        TCGA-78-7154        TCGA-78-7155        TCGA-78-7156 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7158        TCGA-78-7159        TCGA-78-7160        TCGA-78-7161 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7162        TCGA-78-7163        TCGA-78-7166        TCGA-78-7167 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7535        TCGA-78-7536        TCGA-78-7537        TCGA-78-7539 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7540        TCGA-78-7542        TCGA-78-7633        TCGA-80-5607 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-80-5608        TCGA-80-5611        TCGA-83-5908        TCGA-86-6562 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-86-6851        TCGA-86-7701        TCGA-86-7711        TCGA-86-7713 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-86-7953        TCGA-86-7954        TCGA-86-7955        TCGA-91-6828 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-91-6829        TCGA-91-6830        TCGA-91-6831        TCGA-91-6835 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-91-6836        TCGA-91-6840        TCGA-91-6847        TCGA-91-6848 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-91-6849        TCGA-91-7771        TCGA-93-7348        TCGA-95-7039 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-95-7043        TCGA-95-7567        TCGA-95-7944        TCGA-95-7947 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-95-7948        TCGA-97-7546        TCGA-97-7552        TCGA-97-7553 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-97-7554        TCGA-97-7937        TCGA-97-7938        TCGA-97-7941 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-99-7458 
"2Q LOSS WILD-TYPE" 
D44V7, multiclass
D44V8, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1               157
  CLUS_2           1               104
  CLUS_3           1               127
D44V9, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1               170
  CLUS_2           3               195
  CLUS_3           0                98
D44V10, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1               163
  CLUS_2           3               241
  CLUS_3           0                59

Clustering(45) Variable = 3p loss
D45V1, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           0                 5
  CLUS_2           1                 8
  CLUS_3           2                10
  CLUS_4           3                 3
D45V2, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           3                 4
  CLUS_2           2                11
  CLUS_3           1                11
D45V3, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          32               116
  CLUS_2          21               167
  CLUS_3          26                61
  CLUS_4          14                35
D45V4, multiclass
D45V5, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          13                72
  CLUS_2          12                63
  CLUS_3          20                55
D45V6, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           4                19
  CLUS_2          19                70
  CLUS_3          15                50
  CLUS_4           7                51
D45V7, multiclass
D45V8, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          24               134
  CLUS_2          19                86
  CLUS_3          35                93
D45V9, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          24               147
  CLUS_2          49               149
  CLUS_3          17                81
D45V10, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          23               141
  CLUS_2          59               185
  CLUS_3           8                51

Clustering(46) Variable = 3q loss
D46V1, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           0                 5
  CLUS_2           0                 9
  CLUS_3           2                10
  CLUS_4           1                 5
D46V2, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           1                 6
  CLUS_2           2                11
  CLUS_3           0                12
D46V3, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1          21               127
  CLUS_2          12               176
  CLUS_3          13                74
  CLUS_4          10                39
D46V4, multiclass
D46V5, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           5                80
  CLUS_2           9                66
  CLUS_3           9                66
D46V6, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           3                20
  CLUS_2           9                80
  CLUS_3           6                59
  CLUS_4           5                53
D46V7, multiclass
D46V8, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1          19               139
  CLUS_2           9                96
  CLUS_3          18               110
D46V9, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1          17               154
  CLUS_2          28               170
  CLUS_3          10                88
D46V10, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1          14               150
  CLUS_2          38               206
  CLUS_3           3                56

Clustering(47) Variable = 4p loss
D47V1, multiclass
[1] "Remove cluster labels:" "4P LOSS CNV"           
clus
      4P LOSS CNV 4P LOSS WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1595        TCGA-64-1676        TCGA-64-1677 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
D47V2, multiclass
[1] "Remove cluster labels:" "4P LOSS CNV"           
clus
      4P LOSS CNV 4P LOSS WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1595        TCGA-64-1676        TCGA-64-1677 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
D47V3, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1          12               136
  CLUS_2           4               184
  CLUS_3          11                76
  CLUS_4          11                38
D47V4, multiclass
D47V5, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           8                77
  CLUS_2           5                70
  CLUS_3          12                63
D47V6, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           2                21
  CLUS_2           6                83
  CLUS_3          11                54
  CLUS_4           6                52
D47V7, multiclass
D47V8, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           4               154
  CLUS_2           7                98
  CLUS_3          22               106
D47V9, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           7               164
  CLUS_2          28               170
  CLUS_3           2                96
D47V10, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           8               156
  CLUS_2          28               216
  CLUS_3           1                58

Clustering(48) Variable = 4q loss
D48V1, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           0                 5
  CLUS_2           0                 9
  CLUS_3           0                12
  CLUS_4           3                 3
D48V2, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           3                 4
  CLUS_2           0                13
  CLUS_3           0                12
D48V3, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1          15               133
  CLUS_2           1               187
  CLUS_3          17                70
  CLUS_4          12                37
D48V4, multiclass
D48V5, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           9                76
  CLUS_2           7                68
  CLUS_3          12                63
D48V6, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           2                21
  CLUS_2           9                80
  CLUS_3          11                54
  CLUS_4           6                52
D48V7, multiclass
D48V8, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           5               153
  CLUS_2           5               100
  CLUS_3          29                99
D48V9, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           7               164
  CLUS_2          31               167
  CLUS_3           6                92
D48V10, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           7               157
  CLUS_2          35               209
  CLUS_3           2                57

Clustering(49) Variable = 5p loss
D49V1, multiclass
[1] "Remove cluster labels:" "5P LOSS CNV"           
clus
      5P LOSS CNV 5P LOSS WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1595        TCGA-64-1676        TCGA-64-1677 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
D49V2, multiclass
[1] "Remove cluster labels:" "5P LOSS CNV"           
clus
      5P LOSS CNV 5P LOSS WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1595        TCGA-64-1676        TCGA-64-1677 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
D49V3, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           5               143
  CLUS_2           1               187
  CLUS_3           5                82
  CLUS_4           4                45
D49V4, multiclass
D49V5, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           1                84
  CLUS_2           2                73
  CLUS_3           4                71
D49V6, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           0                23
  CLUS_2           2                87
  CLUS_3           3                62
  CLUS_4           2                56
D49V7, multiclass
D49V8, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           2               156
  CLUS_2           3               102
  CLUS_3           9               119
D49V9, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           2               169
  CLUS_2           9               189
  CLUS_3           3                95
D49V10, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           2               162
  CLUS_2          10               234
  CLUS_3           2                57

Clustering(50) Variable = 5q loss
D50V1, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           0                 5
  CLUS_2           1                 8
  CLUS_3           0                12
  CLUS_4           3                 3
D50V2, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           3                 4
  CLUS_2           0                13
  CLUS_3           1                11
D50V3, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          23               125
  CLUS_2           8               180
  CLUS_3          19                68
  CLUS_4           8                41
D50V4, multiclass
D50V5, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          11                74
  CLUS_2           6                69
  CLUS_3          17                58
D50V6, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           4                19
  CLUS_2          10                79
  CLUS_3          15                50
  CLUS_4           5                53
D50V7, multiclass
D50V8, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          13               145
  CLUS_2          15                90
  CLUS_3          23               105
D50V9, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          12               159
  CLUS_2          34               164
  CLUS_3          10                88
D50V10, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          10               154
  CLUS_2          40               204
  CLUS_3           6                53

Clustering(51) Variable = 6p loss
D51V1, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           1                 4
  CLUS_2           1                 8
  CLUS_3           0                12
  CLUS_4           1                 5
D51V2, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           1                 6
  CLUS_2           0                13
  CLUS_3           2                10
D51V3, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1          15               133
  CLUS_2           8               180
  CLUS_3           7                80
  CLUS_4           8                41
D51V4, multiclass
D51V5, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           6                79
  CLUS_2           4                71
  CLUS_3          10                65
D51V6, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           2                21
  CLUS_2           5                84
  CLUS_3           8                57
  CLUS_4           5                53
D51V7, multiclass
D51V8, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1          14               144
  CLUS_2           9                96
  CLUS_3          10               118
D51V9, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1          15               156
  CLUS_2          19               179
  CLUS_3           4                94
D51V10, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1          14               150
  CLUS_2          21               223
  CLUS_3           3                56

Clustering(52) Variable = 6q loss
D52V1, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           1                 4
  CLUS_2           1                 8
  CLUS_3           2                10
  CLUS_4           2                 4
D52V2, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           2                 5
  CLUS_2           2                11
  CLUS_3           2                10
D52V3, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          36               112
  CLUS_2          33               155
  CLUS_3          19                68
  CLUS_4          17                32
D52V4, multiclass
D52V5, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          12                73
  CLUS_2          15                60
  CLUS_3          21                54
D52V6, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           2                21
  CLUS_2          12                77
  CLUS_3          17                48
  CLUS_4          17                41
D52V7, multiclass
D52V8, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          44               114
  CLUS_2          20                85
  CLUS_3          25               103
D52V9, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          42               129
  CLUS_2          45               153
  CLUS_3          17                81
D52V10, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          38               126
  CLUS_2          52               192
  CLUS_3          14                45

Clustering(53) Variable = 7p loss
D53V1, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           0                 5
  CLUS_2           0                 9
  CLUS_3           2                10
  CLUS_4           1                 5
D53V2, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           1                 6
  CLUS_2           2                11
  CLUS_3           0                12
D53V3, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           2               146
  CLUS_2           4               184
  CLUS_3           8                79
  CLUS_4           0                49
D53V4, multiclass
D53V5, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           1                84
  CLUS_2           2                73
  CLUS_3           3                72
D53V6, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           0                23
  CLUS_2           2                87
  CLUS_3           2                63
  CLUS_4           2                56
D53V7, multiclass
D53V8, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           6               152
  CLUS_2           0               105
  CLUS_3           6               122
D53V9, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           7               164
  CLUS_2           7               191
  CLUS_3           0                98
D53V10, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           6               158
  CLUS_2           7               237
  CLUS_3           1                58

Clustering(54) Variable = 7q loss
D54V1, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           1                 4
  CLUS_2           0                 9
  CLUS_3           2                10
  CLUS_4           1                 5
D54V2, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           2                 5
  CLUS_2           2                11
  CLUS_3           0                12
D54V3, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           2               146
  CLUS_2           8               180
  CLUS_3           7                80
  CLUS_4           0                49
D54V4, multiclass
D54V5, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           2                83
  CLUS_2           1                74
  CLUS_3           3                72
D54V6, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           1                22
  CLUS_2           2                87
  CLUS_3           2                63
  CLUS_4           1                57
D54V7, multiclass
D54V8, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           5               153
  CLUS_2           1               104
  CLUS_3           6               122
D54V9, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           6               165
  CLUS_2           8               190
  CLUS_3           3                95
D54V10, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           6               158
  CLUS_2           8               236
  CLUS_3           3                56

Clustering(55) Variable = 8p loss
D55V1, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           4                 1
  CLUS_2           3                 6
  CLUS_3           2                10
  CLUS_4           2                 4
D55V2, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           3                 4
  CLUS_2           2                11
  CLUS_3           6                 6
D55V3, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          69                79
  CLUS_2          18               170
  CLUS_3          24                63
  CLUS_4           7                42
D55V4, multiclass
D55V5, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          23                62
  CLUS_2          14                61
  CLUS_3          24                51
D55V6, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           9                14
  CLUS_2          22                67
  CLUS_3          22                43
  CLUS_4           8                50
D55V7, multiclass
D55V8, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          35               123
  CLUS_2          41                64
  CLUS_3          26               102
D55V9, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          32               139
  CLUS_2          61               137
  CLUS_3          24                74
D55V10, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          33               131
  CLUS_2          75               169
  CLUS_3           9                50

Clustering(56) Variable = 8q loss
D56V1, multiclass
D56V2, multiclass
D56V3, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1          13               135
  CLUS_2           4               184
  CLUS_3           0                87
  CLUS_4           0                49
D56V4, multiclass
D56V5, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           7                78
  CLUS_2           0                75
  CLUS_3           0                75
D56V6, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           3                20
  CLUS_2           4                85
  CLUS_3           0                65
  CLUS_4           0                58
D56V7, multiclass
D56V8, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           5               153
  CLUS_2           7                98
  CLUS_3           1               127
D56V9, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           6               165
  CLUS_2           7               191
  CLUS_3           4                94
D56V10, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           5               159
  CLUS_2           9               235
  CLUS_3           3                56

Clustering(57) Variable = 9p loss
D57V1, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           1                 4
  CLUS_2           1                 8
  CLUS_3           4                 8
  CLUS_4           4                 2
D57V2, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           4                 3
  CLUS_2           4                 9
  CLUS_3           2                10
D57V3, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          50                98
  CLUS_2          35               153
  CLUS_3          46                41
  CLUS_4           8                41
D57V4, multiclass
D57V5, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          23                62
  CLUS_2          22                53
  CLUS_3          28                47
D57V6, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           3                20
  CLUS_2          23                66
  CLUS_3          26                39
  CLUS_4          21                37
D57V7, multiclass
D57V8, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          43               115
  CLUS_2          25                80
  CLUS_3          50                78
D57V9, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          48               123
  CLUS_2          61               137
  CLUS_3          27                71
D57V10, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          46               118
  CLUS_2          75               169
  CLUS_3          15                44

Clustering(58) Variable = 9q loss
D58V1, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           1                 4
  CLUS_2           1                 8
  CLUS_3           4                 8
  CLUS_4           3                 3
D58V2, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           3                 4
  CLUS_2           4                 9
  CLUS_3           2                10
D58V3, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          44               104
  CLUS_2          22               166
  CLUS_3          37                50
  CLUS_4          14                35
D58V4, multiclass
D58V5, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          20                65
  CLUS_2          15                60
  CLUS_3          23                52
D58V6, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           2                21
  CLUS_2          22                67
  CLUS_3          21                44
  CLUS_4          13                45
D58V7, multiclass
D58V8, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          31               127
  CLUS_2          23                82
  CLUS_3          44                84
D58V9, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          34               137
  CLUS_2          58               140
  CLUS_3          22                76
D58V10, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          34               130
  CLUS_2          68               176
  CLUS_3          12                47

Clustering(59) Variable = 10p loss
D59V1, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            1                  4
  CLUS_2            1                  8
  CLUS_3            1                 11
  CLUS_4            1                  5
D59V2, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            1                  6
  CLUS_2            1                 12
  CLUS_3            2                 10
D59V3, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1           18                130
  CLUS_2            4                184
  CLUS_3           10                 77
  CLUS_4            3                 46
D59V4, multiclass
D59V5, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            7                 78
  CLUS_2            2                 73
  CLUS_3           10                 65
D59V6, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            1                 22
  CLUS_2           11                 78
  CLUS_3            6                 59
  CLUS_4            1                 57
D59V7, multiclass
D59V8, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1           10                148
  CLUS_2            8                 97
  CLUS_3           13                115
D59V9, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            7                164
  CLUS_2           16                182
  CLUS_3           12                 86
D59V10, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            6                158
  CLUS_2           20                224
  CLUS_3            9                 50

Clustering(60) Variable = 10q loss
D60V1, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            1                  4
  CLUS_2            1                  8
  CLUS_3            1                 11
  CLUS_4            0                  6
D60V2, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            0                  7
  CLUS_2            1                 12
  CLUS_3            2                 10
D60V3, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           25                123
  CLUS_2            8                180
  CLUS_3            7                 80
  CLUS_4            5                 44
D60V4, multiclass
D60V5, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            9                 76
  CLUS_2            2                 73
  CLUS_3           12                 63
D60V6, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            2                 21
  CLUS_2           12                 77
  CLUS_3            8                 57
  CLUS_4            1                 57
D60V7, multiclass
D60V8, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           13                145
  CLUS_2           11                 94
  CLUS_3           15                113
D60V9, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           13                158
  CLUS_2           18                180
  CLUS_3           13                 85
D60V10, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            9                155
  CLUS_2           25                219
  CLUS_3           10                 49

Clustering(61) Variable = 11p loss
D61V1, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            1                  4
  CLUS_2            1                  8
  CLUS_3            0                 12
  CLUS_4            1                  5
D61V2, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            2                  5
  CLUS_2            0                 13
  CLUS_3            1                 11
D61V3, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1           13                135
  CLUS_2            3                185
  CLUS_3           11                 76
  CLUS_4            5                 44
D61V4, multiclass
D61V5, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            5                 80
  CLUS_2            2                 73
  CLUS_3           13                 62
D61V6, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            0                 23
  CLUS_2            7                 82
  CLUS_3           11                 54
  CLUS_4            2                 56
D61V7, multiclass
D61V8, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            5                153
  CLUS_2           11                 94
  CLUS_3            9                119
D61V9, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            7                164
  CLUS_2           18                180
  CLUS_3            6                 92
D61V10, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            6                158
  CLUS_2           22                222
  CLUS_3            3                 56

Clustering(62) Variable = 11q loss
D62V1, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            1                  4
  CLUS_2            0                  9
  CLUS_3            1                 11
  CLUS_4            1                  5
D62V2, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            2                  5
  CLUS_2            1                 12
  CLUS_3            0                 12
D62V3, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1           13                135
  CLUS_2            3                185
  CLUS_3            8                 79
  CLUS_4            5                 44
D62V4, multiclass
D62V5, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            2                 83
  CLUS_2            2                 73
  CLUS_3           10                 65
D62V6, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            1                 22
  CLUS_2            2                 87
  CLUS_3            9                 56
  CLUS_4            2                 56
D62V7, multiclass
D62V8, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            7                151
  CLUS_2           10                 95
  CLUS_3            6                122
D62V9, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            9                162
  CLUS_2           16                182
  CLUS_3            4                 94
D62V10, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            9                155
  CLUS_2           17                227
  CLUS_3            3                 56

Clustering(63) Variable = 12p loss
D63V1, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            0                  5
  CLUS_2            2                  7
  CLUS_3            1                 11
  CLUS_4            1                  5
D63V2, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            1                  6
  CLUS_2            1                 12
  CLUS_3            2                 10
D63V3, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1           16                132
  CLUS_2           14                174
  CLUS_3            3                 84
  CLUS_4            4                 45
D63V4, multiclass
D63V5, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            8                 77
  CLUS_2            8                 67
  CLUS_3            6                 69
D63V6, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            1                 22
  CLUS_2           11                 78
  CLUS_3            4                 61
  CLUS_4            6                 52
D63V7, multiclass
D63V8, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1           16                142
  CLUS_2            7                 98
  CLUS_3           10                118
D63V9, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1           15                156
  CLUS_2           11                187
  CLUS_3           10                 88
D63V10, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1           15                149
  CLUS_2           17                227
  CLUS_3            4                 55

Clustering(64) Variable = 12q loss
D64V1, multiclass
D64V2, multiclass
D64V3, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1           13                135
  CLUS_2            6                182
  CLUS_3            2                 85
  CLUS_4            2                 47
D64V4, multiclass
D64V5, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            6                 79
  CLUS_2            4                 71
  CLUS_3            4                 71
D64V6, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            2                 21
  CLUS_2            8                 81
  CLUS_3            2                 63
  CLUS_4            2                 56
D64V7, multiclass
D64V8, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            9                149
  CLUS_2            6                 99
  CLUS_3            6                122
D64V9, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            8                163
  CLUS_2            7                191
  CLUS_3            7                 91
D64V10, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            9                155
  CLUS_2           11                233
  CLUS_3            2                 57

Clustering(65) Variable = 13q loss
D65V1, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            3                  2
  CLUS_2            2                  7
  CLUS_3            1                 11
  CLUS_4            3                  3
D65V2, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            4                  3
  CLUS_2            1                 12
  CLUS_3            4                  8
D65V3, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           58                 90
  CLUS_2            4                184
  CLUS_3           31                 56
  CLUS_4           16                 33
D65V4, multiclass
D65V5, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           23                 62
  CLUS_2           13                 62
  CLUS_3           20                 55
D65V6, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            2                 21
  CLUS_2           27                 62
  CLUS_3           20                 45
  CLUS_4            7                 51
D65V7, multiclass
D65V8, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           27                131
  CLUS_2           28                 77
  CLUS_3           35                 93
D65V9, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           28                143
  CLUS_2           61                137
  CLUS_3           19                 79
D65V10, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           27                137
  CLUS_2           67                177
  CLUS_3           14                 45

Clustering(66) Variable = 14q loss
D66V1, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            1                  4
  CLUS_2            0                  9
  CLUS_3            2                 10
  CLUS_4            0                  6
D66V2, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            1                  6
  CLUS_2            2                 11
  CLUS_3            0                 12
D66V3, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           18                130
  CLUS_2           11                177
  CLUS_3           13                 74
  CLUS_4            4                 45
D66V4, multiclass
D66V5, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            8                 77
  CLUS_2            3                 72
  CLUS_3           13                 62
D66V6, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            4                 19
  CLUS_2            4                 85
  CLUS_3           13                 52
  CLUS_4            3                 55
D66V7, multiclass
D66V8, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           14                144
  CLUS_2           12                 93
  CLUS_3           15                113
D66V9, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           12                159
  CLUS_2           27                171
  CLUS_3            7                 91
D66V10, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           13                151
  CLUS_2           30                214
  CLUS_3            3                 56

Clustering(67) Variable = 15q loss
D67V1, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            2                  3
  CLUS_2            2                  7
  CLUS_3            2                 10
  CLUS_4            0                  6
D67V2, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            0                  7
  CLUS_2            2                 11
  CLUS_3            4                  8
D67V3, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           48                100
  CLUS_2            9                179
  CLUS_3           22                 65
  CLUS_4           16                 33
D67V4, multiclass
D67V5, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           18                 67
  CLUS_2           13                 62
  CLUS_3           19                 56
D67V6, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            2                 21
  CLUS_2           25                 64
  CLUS_3           17                 48
  CLUS_4            6                 52
D67V7, multiclass
D67V8, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           18                140
  CLUS_2           32                 73
  CLUS_3           30                 98
D67V9, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           19                152
  CLUS_2           55                143
  CLUS_3           20                 78
D67V10, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           17                147
  CLUS_2           64                180
  CLUS_3           13                 46

Clustering(68) Variable = 16p loss
D68V1, multiclass
[1] "Remove cluster labels:" "16P LOSS CNV"          
clus
      16P LOSS CNV 16P LOSS WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1678         TCGA-64-1680 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-67-3774 
"16P LOSS WILD-TYPE" 
D68V2, multiclass
[1] "Remove cluster labels:" "16P LOSS CNV"          
clus
      16P LOSS CNV 16P LOSS WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1678         TCGA-64-1680 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-67-3774 
"16P LOSS WILD-TYPE" 
D68V3, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1           15                133
  CLUS_2            4                184
  CLUS_3           13                 74
  CLUS_4            5                 44
D68V4, multiclass
D68V5, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            8                 77
  CLUS_2            2                 73
  CLUS_3           10                 65
D68V6, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            1                 22
  CLUS_2            9                 80
  CLUS_3            8                 57
  CLUS_4            2                 56
D68V7, multiclass
D68V8, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            8                150
  CLUS_2            8                 97
  CLUS_3           15                113
D68V9, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            9                162
  CLUS_2           22                176
  CLUS_3            6                 92
D68V10, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            7                157
  CLUS_2           24                220
  CLUS_3            6                 53

Clustering(69) Variable = 16q loss
D69V1, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            3                  2
  CLUS_2            0                  9
  CLUS_3            2                 10
  CLUS_4            0                  6
D69V2, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            1                  6
  CLUS_2            2                 11
  CLUS_3            2                 10
D69V3, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           28                120
  CLUS_2            6                182
  CLUS_3           15                 72
  CLUS_4            7                 42
D69V4, multiclass
D69V5, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            9                 76
  CLUS_2            6                 69
  CLUS_3           19                 56
D69V6, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            5                 18
  CLUS_2           10                 79
  CLUS_3           16                 49
  CLUS_4            3                 55
D69V7, multiclass
D69V8, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           15                143
  CLUS_2           16                 89
  CLUS_3           20                108
D69V9, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           15                156
  CLUS_2           34                164
  CLUS_3            7                 91
D69V10, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           14                150
  CLUS_2           35                209
  CLUS_3            7                 52

Clustering(70) Variable = 17p loss
D70V1, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            4                  1
  CLUS_2            2                  7
  CLUS_3            3                  9
  CLUS_4            3                  3
D70V2, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            4                  3
  CLUS_2            3                 10
  CLUS_3            5                  7
D70V3, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           53                 95
  CLUS_2           23                165
  CLUS_3           20                 67
  CLUS_4           13                 36
D70V4, multiclass
D70V5, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           29                 56
  CLUS_2           13                 62
  CLUS_3           19                 56
D70V6, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            5                 18
  CLUS_2           30                 59
  CLUS_3           15                 50
  CLUS_4           11                 47
D70V7, multiclass
D70V8, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           36                122
  CLUS_2           30                 75
  CLUS_3           28                100
D70V9, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           37                134
  CLUS_2           51                147
  CLUS_3           21                 77
D70V10, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           34                130
  CLUS_2           60                184
  CLUS_3           15                 44

Clustering(71) Variable = 17q loss
D71V1, multiclass
[1] "Remove cluster labels:" "17Q LOSS CNV"          
clus
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-44-2666         TCGA-44-2668         TCGA-44-3398 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-44-3918         TCGA-44-3919         TCGA-44-4112 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-55-1592         TCGA-55-1594         TCGA-55-1595 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-67-3774 
"17Q LOSS WILD-TYPE" 
D71V2, multiclass
[1] "Remove cluster labels:" "17Q LOSS CNV"          
clus
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-44-2666         TCGA-44-2668         TCGA-44-3398 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-44-3918         TCGA-44-3919         TCGA-44-4112 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-55-1592         TCGA-55-1594         TCGA-55-1595 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-67-3774 
"17Q LOSS WILD-TYPE" 
D71V3, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            9                139
  CLUS_2            3                185
  CLUS_3            3                 84
  CLUS_4            2                 47
D71V4, multiclass
D71V5, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            8                 77
  CLUS_2            1                 74
  CLUS_3            3                 72
D71V6, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            1                 22
  CLUS_2            6                 83
  CLUS_3            3                 62
  CLUS_4            2                 56
D71V7, multiclass
D71V8, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            7                151
  CLUS_2            6                 99
  CLUS_3            2                126
D71V9, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            5                166
  CLUS_2            8                190
  CLUS_3            4                 94
D71V10, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            2                162
  CLUS_2           10                234
  CLUS_3            5                 54

Clustering(72) Variable = 18p loss
D72V1, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            0                  5
  CLUS_2            1                  8
  CLUS_3            1                 11
  CLUS_4            2                  4
D72V2, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            2                  5
  CLUS_2            1                 12
  CLUS_3            1                 11
D72V3, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           35                113
  CLUS_2           14                174
  CLUS_3           22                 65
  CLUS_4            4                 45
D72V4, multiclass
D72V5, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           15                 70
  CLUS_2           11                 64
  CLUS_3           12                 63
D72V6, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            5                 18
  CLUS_2           18                 71
  CLUS_3           10                 55
  CLUS_4            5                 53
D72V7, multiclass
D72V8, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           23                135
  CLUS_2           21                 84
  CLUS_3           16                112
D72V9, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           25                146
  CLUS_2           34                164
  CLUS_3           13                 85
D72V10, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           26                138
  CLUS_2           36                208
  CLUS_3           10                 49

Clustering(73) Variable = 18q loss
D73V1, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            0                  5
  CLUS_2            1                  8
  CLUS_3            1                 11
  CLUS_4            2                  4
D73V2, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            2                  5
  CLUS_2            1                 12
  CLUS_3            1                 11
D73V3, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           52                 96
  CLUS_2           22                166
  CLUS_3           31                 56
  CLUS_4            3                 46
D73V4, multiclass
D73V5, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           25                 60
  CLUS_2           14                 61
  CLUS_3           18                 57
D73V6, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            8                 15
  CLUS_2           24                 65
  CLUS_3           17                 48
  CLUS_4            8                 50
D73V7, multiclass
D73V8, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           32                126
  CLUS_2           34                 71
  CLUS_3           23                105
D73V9, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           31                140
  CLUS_2           53                145
  CLUS_3           21                 77
D73V10, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           36                128
  CLUS_2           55                189
  CLUS_3           14                 45

Clustering(74) Variable = 19p loss
D74V1, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                  4
  CLUS_2            2                  7
  CLUS_3            3                  9
  CLUS_4            3                  3
D74V2, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            3                  4
  CLUS_2            3                 10
  CLUS_3            3                  9
D74V3, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1           32                116
  CLUS_2           22                166
  CLUS_3           41                 46
  CLUS_4           17                 32
D74V4, multiclass
D74V5, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1           22                 63
  CLUS_2           22                 53
  CLUS_3           19                 56
D74V6, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            4                 19
  CLUS_2           24                 65
  CLUS_3           17                 48
  CLUS_4           18                 40
D74V7, multiclass
D74V8, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1           35                123
  CLUS_2           23                 82
  CLUS_3           41                 87
D74V9, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1           34                137
  CLUS_2           59                139
  CLUS_3           14                 84
D74V10, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1           35                129
  CLUS_2           66                178
  CLUS_3            6                 53

Clustering(75) Variable = 19q loss
D75V1, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            0                  5
  CLUS_2            2                  7
  CLUS_3            2                 10
  CLUS_4            2                  4
D75V2, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            2                  5
  CLUS_2            2                 11
  CLUS_3            2                 10
D75V3, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1           27                121
  CLUS_2           12                176
  CLUS_3           21                 66
  CLUS_4            7                 42
D75V4, multiclass
D75V5, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1           16                 69
  CLUS_2           12                 63
  CLUS_3           11                 64
D75V6, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            2                 21
  CLUS_2           18                 71
  CLUS_3            8                 57
  CLUS_4           11                 47
D75V7, multiclass
D75V8, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1           19                139
  CLUS_2           16                 89
  CLUS_3           22                106
D75V9, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1           18                153
  CLUS_2           37                161
  CLUS_3            8                 90
D75V10, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1           18                146
  CLUS_2           41                203
  CLUS_3            4                 55

Clustering(76) Variable = 20p loss
D76V1, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            1                  4
  CLUS_2            0                  9
  CLUS_3            1                 11
  CLUS_4            2                  4
D76V2, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            2                  5
  CLUS_2            1                 12
  CLUS_3            1                 11
D76V3, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1           30                118
  CLUS_2           11                177
  CLUS_3           16                 71
  CLUS_4            4                 45
D76V4, multiclass
D76V5, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1           19                 66
  CLUS_2            4                 71
  CLUS_3           12                 63
D76V6, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            4                 19
  CLUS_2           20                 69
  CLUS_3            8                 57
  CLUS_4            3                 55
D76V7, multiclass
D76V8, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1           16                142
  CLUS_2           19                 86
  CLUS_3           17                111
D76V9, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1           20                151
  CLUS_2           28                170
  CLUS_3           11                 87
D76V10, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1           14                150
  CLUS_2           35                209
  CLUS_3           10                 49

Clustering(77) Variable = 20q loss
D77V1, multiclass
[1] "Remove cluster labels:" "20Q LOSS CNV"          
clus
      20Q LOSS CNV 20Q LOSS WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1680         TCGA-67-3770 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3774 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D77V2, multiclass
[1] "Remove cluster labels:" "20Q LOSS CNV"          
clus
      20Q LOSS CNV 20Q LOSS WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1680         TCGA-67-3770 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3774 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D77V3, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            5                143
  CLUS_2            8                180
  CLUS_3            7                 80
  CLUS_4            4                 45
D77V4, multiclass
D77V5, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            7                 78
  CLUS_2            2                 73
  CLUS_3            4                 71
D77V6, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            3                 20
  CLUS_2            3                 86
  CLUS_3            4                 61
  CLUS_4            3                 55
D77V7, multiclass
D77V8, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1           11                147
  CLUS_2            3                102
  CLUS_3            6                122
D77V9, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1           10                161
  CLUS_2           11                187
  CLUS_3            3                 95
D77V10, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            6                158
  CLUS_2           14                230
  CLUS_3            4                 55

Clustering(78) Variable = 21q loss
D78V1, multiclass
[1] "Remove cluster labels:" "21Q LOSS CNV"          
clus
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1595         TCGA-55-1596 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-64-1676         TCGA-64-1677         TCGA-64-1678 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-64-1680         TCGA-67-3770         TCGA-67-3771 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-67-3772         TCGA-67-3773         TCGA-67-3774 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
D78V2, multiclass
[1] "Remove cluster labels:" "21Q LOSS CNV"          
clus
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1595         TCGA-55-1596 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-64-1676         TCGA-64-1677         TCGA-64-1678 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-64-1680         TCGA-67-3770         TCGA-67-3771 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-67-3772         TCGA-67-3773         TCGA-67-3774 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
D78V3, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1           13                135
  CLUS_2            8                180
  CLUS_3           30                 57
  CLUS_4           15                 34
D78V4, multiclass
D78V5, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            8                 77
  CLUS_2           10                 65
  CLUS_3           16                 59
D78V6, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            2                 21
  CLUS_2            6                 83
  CLUS_3           15                 50
  CLUS_4           11                 47
D78V7, multiclass
D78V8, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1           13                145
  CLUS_2            7                 98
  CLUS_3           37                 91
D78V9, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1           12                159
  CLUS_2           44                154
  CLUS_3            8                 90
D78V10, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1           11                153
  CLUS_2           52                192
  CLUS_3            1                 58

Clustering(79) Variable = 22q loss
D79V1, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            2                  3
  CLUS_2            1                  8
  CLUS_3            1                 11
  CLUS_4            0                  6
D79V2, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            0                  7
  CLUS_2            1                 12
  CLUS_3            3                  9
D79V3, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           39                109
  CLUS_2           10                178
  CLUS_3           24                 63
  CLUS_4           17                 32
D79V4, multiclass
D79V5, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           20                 65
  CLUS_2           10                 65
  CLUS_3           26                 49
D79V6, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            4                 19
  CLUS_2           19                 70
  CLUS_3           25                 40
  CLUS_4            8                 50
D79V7, multiclass
D79V8, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           22                136
  CLUS_2           20                 85
  CLUS_3           37                 91
D79V9, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           21                150
  CLUS_2           54                144
  CLUS_3           13                 85
D79V10, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           21                143
  CLUS_2           61                183
  CLUS_3            6                 53

Clustering(80) Variable = Xq loss
D80V1, multiclass
[1] "Remove cluster labels:" "XQ LOSS CNV"           
clus
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                2                30 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1594 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-55-1596        TCGA-64-1676        TCGA-64-1677        TCGA-64-1678 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-64-1680        TCGA-67-3770        TCGA-67-3771        TCGA-67-3772 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-67-3773        TCGA-67-3774 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D80V2, multiclass
[1] "Remove cluster labels:" "XQ LOSS CNV"           
clus
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                2                30 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1594 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-55-1596        TCGA-64-1676        TCGA-64-1677        TCGA-64-1678 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-64-1680        TCGA-67-3770        TCGA-67-3771        TCGA-67-3772 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-67-3773        TCGA-67-3774 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D80V3, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           4               144
  CLUS_2           3               185
  CLUS_3           1                86
  CLUS_4           3                46
D80V4, multiclass
D80V5, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           1                84
  CLUS_2           2                73
  CLUS_3           2                73
D80V6, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           0                23
  CLUS_2           1                88
  CLUS_3           3                62
  CLUS_4           1                57
D80V7, multiclass
D80V8, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           3               155
  CLUS_2           1               104
  CLUS_3           5               123
D80V9, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           3               168
  CLUS_2           6               192
  CLUS_3           2                96
D80V10, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           3               161
  CLUS_2           8               236
  CLUS_3           0                59
                     V1                      V2                      V3 
            "MRNA_CNMF"    "MRNA_CHIERARCHICAL"               "CN_CNMF" 
                     V4                      V5                      V6 
     "METHLYATION_CNMF"             "RPPA_CNMF"    "RPPA_CHIERARCHICAL" 
                     V7                      V8                      V9 
         "MRNASEQ_CNMF" "MRNASEQ_CHIERARCHICAL"           "MIRSEQ_CNMF" 
                    V10 
 "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
