
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/LGG-TP/4431268/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/LGG-TP/4431190/LGG-TP.transferedmergedcluster.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=LGG-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=LGG-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=296, in cluster file=269, common to both=269
[1] "Reduce the number of clustering variables from 80 to 60."
[1]  60 269
[1] "1p gain"
[1] 3
      1P GAIN CNV 1P GAIN WILD-TYPE 
                8               261 
      1P GAIN CNV 1P GAIN WILD-TYPE 
                8               261 
[1] "1q gain"
[1] 3
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
               10               259 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
               10               259 
[1] "3p gain"
[1] 3
      3P GAIN CNV 3P GAIN WILD-TYPE 
                3               266 
      3P GAIN CNV 3P GAIN WILD-TYPE 
                3               266 
[1] "3q gain"
[1] 3
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                3               266 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                3               266 
[1] "4p gain"
[1] 3
      4P GAIN CNV 4P GAIN WILD-TYPE 
                4               265 
      4P GAIN CNV 4P GAIN WILD-TYPE 
                4               265 
[1] "6p gain"
[1] 3
      6P GAIN CNV 6P GAIN WILD-TYPE 
                3               266 
      6P GAIN CNV 6P GAIN WILD-TYPE 
                3               266 
[1] "7p gain"
[1] 3
      7P GAIN CNV 7P GAIN WILD-TYPE 
               50               219 
      7P GAIN CNV 7P GAIN WILD-TYPE 
               50               219 
[1] "7q gain"
[1] 3
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               68               201 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               68               201 
[1] "8p gain"
[1] 3
      8P GAIN CNV 8P GAIN WILD-TYPE 
               17               252 
      8P GAIN CNV 8P GAIN WILD-TYPE 
               17               252 
[1] "8q gain"
[1] 3
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               22               247 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               22               247 
[1] "9p gain"
[1] 3
      9P GAIN CNV 9P GAIN WILD-TYPE 
                6               263 
      9P GAIN CNV 9P GAIN WILD-TYPE 
                6               263 
[1] "9q gain"
[1] 3
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                9               260 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                9               260 
[1] "10p gain"
[1] 3
      10P GAIN CNV 10P GAIN WILD-TYPE 
                24                245 
      10P GAIN CNV 10P GAIN WILD-TYPE 
                24                245 
[1] "11p gain"
[1] 3
      11P GAIN CNV 11P GAIN WILD-TYPE 
                11                258 
      11P GAIN CNV 11P GAIN WILD-TYPE 
                11                258 
[1] "11q gain"
[1] 3
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                15                254 
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                15                254 
[1] "12p gain"
[1] 3
      12P GAIN CNV 12P GAIN WILD-TYPE 
                13                256 
      12P GAIN CNV 12P GAIN WILD-TYPE 
                13                256 
[1] "12q gain"
[1] 3
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 5                264 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 5                264 
[1] "18p gain"
[1] 3
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 7                262 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 7                262 
[1] "18q gain"
[1] 3
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 4                265 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 4                265 
[1] "19p gain"
[1] 3
      19P GAIN CNV 19P GAIN WILD-TYPE 
                17                252 
      19P GAIN CNV 19P GAIN WILD-TYPE 
                17                252 
[1] "19q gain"
[1] 3
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                12                257 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                12                257 
[1] "20p gain"
[1] 3
      20P GAIN CNV 20P GAIN WILD-TYPE 
                20                249 
      20P GAIN CNV 20P GAIN WILD-TYPE 
                20                249 
[1] "20q gain"
[1] 3
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                20                249 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                20                249 
[1] "21q gain"
[1] 3
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 6                263 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 6                263 
[1] "1p loss"
[1] 3
      1P LOSS CNV 1P LOSS WILD-TYPE 
               77               192 
      1P LOSS CNV 1P LOSS WILD-TYPE 
               77               192 
[1] "1q loss"
[1] 3
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
               10               259 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
               10               259 
[1] "2p loss"
[1] 3
      2P LOSS CNV 2P LOSS WILD-TYPE 
                6               263 
      2P LOSS CNV 2P LOSS WILD-TYPE 
                6               263 
[1] "2q loss"
[1] 3
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                4               265 
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                4               265 
[1] "3p loss"
[1] 3
      3P LOSS CNV 3P LOSS WILD-TYPE 
               10               259 
      3P LOSS CNV 3P LOSS WILD-TYPE 
               10               259 
[1] "3q loss"
[1] 3
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
               13               256 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
               13               256 
[1] "4p loss"
[1] 3
      4P LOSS CNV 4P LOSS WILD-TYPE 
               18               251 
      4P LOSS CNV 4P LOSS WILD-TYPE 
               18               251 
[1] "4q loss"
[1] 3
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               28               241 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               28               241 
[1] "5p loss"
[1] 3
      5P LOSS CNV 5P LOSS WILD-TYPE 
               13               256 
      5P LOSS CNV 5P LOSS WILD-TYPE 
               13               256 
[1] "5q loss"
[1] 3
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
               11               258 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
               11               258 
[1] "6p loss"
[1] 3
      6P LOSS CNV 6P LOSS WILD-TYPE 
               10               259 
      6P LOSS CNV 6P LOSS WILD-TYPE 
               10               259 
[1] "6q loss"
[1] 3
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               32               237 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               32               237 
[1] "8p loss"
[1] 3
      8P LOSS CNV 8P LOSS WILD-TYPE 
                6               263 
      8P LOSS CNV 8P LOSS WILD-TYPE 
                6               263 
[1] "8q loss"
[1] 3
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                4               265 
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                4               265 
[1] "9p loss"
[1] 3
      9P LOSS CNV 9P LOSS WILD-TYPE 
               49               220 
      9P LOSS CNV 9P LOSS WILD-TYPE 
               49               220 
[1] "9q loss"
[1] 3
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
                7               262 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
                7               262 
[1] "10p loss"
[1] 3
      10P LOSS CNV 10P LOSS WILD-TYPE 
                36                233 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                36                233 
[1] "10q loss"
[1] 3
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                38                231 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                38                231 
[1] "11p loss"
[1] 3
      11P LOSS CNV 11P LOSS WILD-TYPE 
                25                244 
      11P LOSS CNV 11P LOSS WILD-TYPE 
                25                244 
[1] "11q loss"
[1] 3
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 7                262 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 7                262 
[1] "12p loss"
[1] 3
      12P LOSS CNV 12P LOSS WILD-TYPE 
                 4                265 
      12P LOSS CNV 12P LOSS WILD-TYPE 
                 4                265 
[1] "12q loss"
[1] 3
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                11                258 
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                11                258 
[1] "13q loss"
[1] 3
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                31                238 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                31                238 
[1] "14q loss"
[1] 3
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                28                241 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                28                241 
[1] "15q loss"
[1] 3
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                16                253 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                16                253 
[1] "16p loss"
[1] 3
      16P LOSS CNV 16P LOSS WILD-TYPE 
                 3                266 
      16P LOSS CNV 16P LOSS WILD-TYPE 
                 3                266 
[1] "16q loss"
[1] 3
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 7                262 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 7                262 
[1] "17p loss"
[1] 3
      17P LOSS CNV 17P LOSS WILD-TYPE 
                 4                265 
      17P LOSS CNV 17P LOSS WILD-TYPE 
                 4                265 
[1] "18p loss"
[1] 3
      18P LOSS CNV 18P LOSS WILD-TYPE 
                21                248 
      18P LOSS CNV 18P LOSS WILD-TYPE 
                21                248 
[1] "18q loss"
[1] 3
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                20                249 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                20                249 
[1] "19p loss"
[1] 3
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 7                262 
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 7                262 
[1] "19q loss"
[1] 3
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                85                184 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                85                184 
[1] "20p loss"
[1] 3
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 3                266 
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 3                266 
[1] "21q loss"
[1] 3
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                11                258 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                11                258 
[1] "22q loss"
[1] 3
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                20                249 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                20                249 
[1] "Xq loss"
[1] 3
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                6               263 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                6               263 
[1] "data2feature, selection="
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 12 rows and 269 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'RPPA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MIRSEQ_MATURE_CNMF':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 269 columns, 0 survival variables, and 12 non-survival variables.
MRNA_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
CN_CNMF, nv=4, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=8, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain
D1V1, multiclass
D1V2, multiclass
D1V3, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           1                51
  CLUS_2           3                54
  CLUS_3           4                50
  CLUS_4           0               106
D1V4, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           3               119
  CLUS_2           5                37
  CLUS_3           0                66
  CLUS_4           0                34
D1V5, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           1                51
  CLUS_2           4                58
  CLUS_3           1                67
  CLUS_4           0                74
D1V6, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           4               125
  CLUS_3           2               117
D1V7, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           8                86
  CLUS_2           0                78
  CLUS_3           0                97
D1V8, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           0                36
  CLUS_2           8               133
  CLUS_3           0                92
D1V9, multiclass
D1V10, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           1                13
  CLUS_2           7               138
  CLUS_3           0               109
D1V11, multiclass
D1V12, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           5                37
  CLUS_2           2               103
  CLUS_3           1               120

Clustering(2) Variable = 1q gain
D2V1, multiclass
D2V2, multiclass
D2V3, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           0                52
  CLUS_2           4                53
  CLUS_3           6                48
  CLUS_4           0               106
D2V4, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           5               117
  CLUS_2           5                37
  CLUS_3           0                66
  CLUS_4           0                34
D2V5, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           1                51
  CLUS_2           4                58
  CLUS_3           1                67
  CLUS_4           2                72
D2V6, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           4               125
  CLUS_3           4               115
D2V7, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           7                87
  CLUS_2           1                77
  CLUS_3           2                95
D2V8, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           0                36
  CLUS_2           8               133
  CLUS_3           2                90
D2V9, multiclass
D2V10, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           1                13
  CLUS_2           7               138
  CLUS_3           2               107
D2V11, multiclass
D2V12, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           4                38
  CLUS_2           3               102
  CLUS_3           3               118

Clustering(3) Variable = 3p gain
D3V1, multiclass
[1] "Remove cluster labels:" "3P GAIN CNV"           
clus
      3P GAIN CNV 3P GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DH-5144        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D3V2, multiclass
[1] "Remove cluster labels:" "3P GAIN CNV"           
clus
      3P GAIN CNV 3P GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DH-5144        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D3V3, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           0                52
  CLUS_2           1                56
  CLUS_3           1                53
  CLUS_4           1               105
D3V4, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           1               121
  CLUS_2           1                41
  CLUS_3           1                65
  CLUS_4           0                34
D3V5, multiclass
[1] "Remove cluster labels:" "3P GAIN CNV"           
clus
      3P GAIN CNV 3P GAIN WILD-TYPE 
                2               254 
       TCGA-CS-4938        TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CS-5390        TCGA-CS-5393        TCGA-CS-5394        TCGA-CS-5396 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CS-5397        TCGA-CS-6186        TCGA-CS-6188        TCGA-CS-6665 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CS-6666        TCGA-CS-6669        TCGA-CS-6670        TCGA-DB-5270 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5279        TCGA-DB-5280 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DB-5281        TCGA-DB-A4X9        TCGA-DB-A4XA        TCGA-DB-A4XB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DB-A4XC        TCGA-DB-A4XD        TCGA-DB-A4XE        TCGA-DB-A4XF 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DB-A4XG        TCGA-DB-A4XH        TCGA-DH-5140        TCGA-DH-5141 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144        TCGA-DU-5847 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-5849        TCGA-DU-5851        TCGA-DU-5852        TCGA-DU-5853 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-5854        TCGA-DU-5855        TCGA-DU-5870        TCGA-DU-5871 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-5872        TCGA-DU-5874        TCGA-DU-6392        TCGA-DU-6393 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-6394        TCGA-DU-6395        TCGA-DU-6396        TCGA-DU-6397 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-6399        TCGA-DU-6400        TCGA-DU-6401        TCGA-DU-6402 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-6403        TCGA-DU-6404        TCGA-DU-6405        TCGA-DU-6406 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-6407        TCGA-DU-6408        TCGA-DU-6410        TCGA-DU-6542 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-7006        TCGA-DU-7007        TCGA-DU-7008        TCGA-DU-7009 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-7010        TCGA-DU-7011        TCGA-DU-7012        TCGA-DU-7013 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-7014        TCGA-DU-7015        TCGA-DU-7018        TCGA-DU-7019 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-7290        TCGA-DU-7292        TCGA-DU-7294        TCGA-DU-7298 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-7300        TCGA-DU-7301        TCGA-DU-7302        TCGA-DU-7304 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-7306        TCGA-DU-7309        TCGA-DU-8158        TCGA-DU-8161 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-8162        TCGA-DU-8163        TCGA-DU-8164        TCGA-DU-8165 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-8166        TCGA-DU-8167        TCGA-DU-8168        TCGA-DU-A5TP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-A5TR        TCGA-DU-A5TS        TCGA-DU-A5TT        TCGA-DU-A5TU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-A5TW        TCGA-DU-A5TY        TCGA-E1-5302        TCGA-E1-5303 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E1-5305        TCGA-E1-5307        TCGA-E1-5311        TCGA-E1-5318 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E1-5319        TCGA-E1-5322        TCGA-EZ-7264        TCGA-FG-5962 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FG-5963        TCGA-FG-5964        TCGA-FG-5965        TCGA-FG-6688 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FG-6689        TCGA-FG-6690        TCGA-FG-6691        TCGA-FG-7634 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FG-7636        TCGA-FG-7638        TCGA-FG-7641        TCGA-FG-7643 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FG-8181        TCGA-FG-8182        TCGA-FG-8185        TCGA-FG-8186 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FG-8187        TCGA-FG-8188        TCGA-FG-8189        TCGA-FG-8191 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FG-A4MT        TCGA-FG-A4MU        TCGA-FG-A4MW        TCGA-FG-A4MX 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FG-A4MY        TCGA-FG-A60J        TCGA-HT-7467        TCGA-HT-7468 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7469        TCGA-HT-7470        TCGA-HT-7471        TCGA-HT-7472 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7473        TCGA-HT-7474        TCGA-HT-7475        TCGA-HT-7476 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7477        TCGA-HT-7478        TCGA-HT-7479        TCGA-HT-7480 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7481        TCGA-HT-7482        TCGA-HT-7483        TCGA-HT-7485 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7601        TCGA-HT-7602        TCGA-HT-7603        TCGA-HT-7604 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7605        TCGA-HT-7606        TCGA-HT-7607        TCGA-HT-7608 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7609        TCGA-HT-7610        TCGA-HT-7611        TCGA-HT-7616 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7620        TCGA-HT-7676        TCGA-HT-7677        TCGA-HT-7680 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7681        TCGA-HT-7684        TCGA-HT-7686        TCGA-HT-7687 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7688        TCGA-HT-7689        TCGA-HT-7690        TCGA-HT-7691 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7692        TCGA-HT-7693        TCGA-HT-7694        TCGA-HT-7695 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7854        TCGA-HT-7855        TCGA-HT-7856        TCGA-HT-7857 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7858        TCGA-HT-7860        TCGA-HT-7873        TCGA-HT-7874 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7875        TCGA-HT-7877        TCGA-HT-7879        TCGA-HT-7880 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7881        TCGA-HT-7882        TCGA-HT-7884        TCGA-HT-7902 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-8010        TCGA-HT-8011        TCGA-HT-8012        TCGA-HT-8013 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-8015        TCGA-HT-8018        TCGA-HT-8019        TCGA-HT-8104 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-8105        TCGA-HT-8106        TCGA-HT-8107        TCGA-HT-8109 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-8110        TCGA-HT-8111        TCGA-HT-8113        TCGA-HT-8114 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-8564        TCGA-HT-A4DV        TCGA-HT-A5R5        TCGA-HT-A5R7 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-A5R9        TCGA-HT-A5RB        TCGA-HW-7486        TCGA-HW-7487 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HW-7489        TCGA-HW-7490        TCGA-HW-7491        TCGA-HW-7493 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HW-7495        TCGA-HW-8319        TCGA-HW-8320        TCGA-HW-8321 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HW-8322        TCGA-HW-A5KJ        TCGA-HW-A5KK        TCGA-HW-A5KM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IK-7675        TCGA-IK-8125        TCGA-P5-A5ET        TCGA-P5-A5EU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-P5-A5EV        TCGA-P5-A5EW        TCGA-P5-A5EX        TCGA-P5-A5EY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-P5-A5EZ        TCGA-P5-A5F0        TCGA-P5-A5F1        TCGA-P5-A5F2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-P5-A5F4        TCGA-P5-A5F6 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D3V6, multiclass
[1] "Remove cluster labels:" "3P GAIN CNV"           
clus
      3P GAIN CNV 3P GAIN WILD-TYPE 
                2               254 
       TCGA-CS-4938        TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CS-5390        TCGA-CS-5393        TCGA-CS-5394        TCGA-CS-5396 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CS-5397        TCGA-CS-6186        TCGA-CS-6188        TCGA-CS-6665 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CS-6666        TCGA-CS-6669        TCGA-CS-6670        TCGA-DB-5270 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5279        TCGA-DB-5280 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DB-5281        TCGA-DB-A4X9        TCGA-DB-A4XA        TCGA-DB-A4XB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DB-A4XC        TCGA-DB-A4XD        TCGA-DB-A4XE        TCGA-DB-A4XF 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DB-A4XG        TCGA-DB-A4XH        TCGA-DH-5140        TCGA-DH-5141 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144        TCGA-DU-5847 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-5849        TCGA-DU-5851        TCGA-DU-5852        TCGA-DU-5853 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-5854        TCGA-DU-5855        TCGA-DU-5870        TCGA-DU-5871 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-5872        TCGA-DU-5874        TCGA-DU-6392        TCGA-DU-6393 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-6394        TCGA-DU-6395        TCGA-DU-6396        TCGA-DU-6397 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-6399        TCGA-DU-6400        TCGA-DU-6401        TCGA-DU-6402 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-6403        TCGA-DU-6404        TCGA-DU-6405        TCGA-DU-6406 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-6407        TCGA-DU-6408        TCGA-DU-6410        TCGA-DU-6542 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-7006        TCGA-DU-7007        TCGA-DU-7008        TCGA-DU-7009 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-7010        TCGA-DU-7011        TCGA-DU-7012        TCGA-DU-7013 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-7014        TCGA-DU-7015        TCGA-DU-7018        TCGA-DU-7019 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-7290        TCGA-DU-7292        TCGA-DU-7294        TCGA-DU-7298 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-7300        TCGA-DU-7301        TCGA-DU-7302        TCGA-DU-7304 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-7306        TCGA-DU-7309        TCGA-DU-8158        TCGA-DU-8161 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-8162        TCGA-DU-8163        TCGA-DU-8164        TCGA-DU-8165 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-8166        TCGA-DU-8167        TCGA-DU-8168        TCGA-DU-A5TP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-A5TR        TCGA-DU-A5TS        TCGA-DU-A5TT        TCGA-DU-A5TU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DU-A5TW        TCGA-DU-A5TY        TCGA-E1-5302        TCGA-E1-5303 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E1-5305        TCGA-E1-5307        TCGA-E1-5311        TCGA-E1-5318 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-E1-5319        TCGA-E1-5322        TCGA-EZ-7264        TCGA-FG-5962 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FG-5963        TCGA-FG-5964        TCGA-FG-5965        TCGA-FG-6688 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FG-6689        TCGA-FG-6690        TCGA-FG-6691        TCGA-FG-7634 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FG-7636        TCGA-FG-7638        TCGA-FG-7641        TCGA-FG-7643 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FG-8181        TCGA-FG-8182        TCGA-FG-8185        TCGA-FG-8186 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FG-8187        TCGA-FG-8188        TCGA-FG-8189        TCGA-FG-8191 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FG-A4MT        TCGA-FG-A4MU        TCGA-FG-A4MW        TCGA-FG-A4MX 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FG-A4MY        TCGA-FG-A60J        TCGA-HT-7467        TCGA-HT-7468 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7469        TCGA-HT-7470        TCGA-HT-7471        TCGA-HT-7472 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7473        TCGA-HT-7474        TCGA-HT-7475        TCGA-HT-7476 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7477        TCGA-HT-7478        TCGA-HT-7479        TCGA-HT-7480 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7481        TCGA-HT-7482        TCGA-HT-7483        TCGA-HT-7485 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7601        TCGA-HT-7602        TCGA-HT-7603        TCGA-HT-7604 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7605        TCGA-HT-7606        TCGA-HT-7607        TCGA-HT-7608 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7609        TCGA-HT-7610        TCGA-HT-7611        TCGA-HT-7616 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7620        TCGA-HT-7676        TCGA-HT-7677        TCGA-HT-7680 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7681        TCGA-HT-7684        TCGA-HT-7686        TCGA-HT-7687 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7688        TCGA-HT-7689        TCGA-HT-7690        TCGA-HT-7691 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7692        TCGA-HT-7693        TCGA-HT-7694        TCGA-HT-7695 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7854        TCGA-HT-7855        TCGA-HT-7856        TCGA-HT-7857 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7858        TCGA-HT-7860        TCGA-HT-7873        TCGA-HT-7874 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7875        TCGA-HT-7877        TCGA-HT-7879        TCGA-HT-7880 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-7881        TCGA-HT-7882        TCGA-HT-7884        TCGA-HT-7902 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-8010        TCGA-HT-8011        TCGA-HT-8012        TCGA-HT-8013 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-8015        TCGA-HT-8018        TCGA-HT-8019        TCGA-HT-8104 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-8105        TCGA-HT-8106        TCGA-HT-8107        TCGA-HT-8109 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-8110        TCGA-HT-8111        TCGA-HT-8113        TCGA-HT-8114 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-8564        TCGA-HT-A4DV        TCGA-HT-A5R5        TCGA-HT-A5R7 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HT-A5R9        TCGA-HT-A5RB        TCGA-HW-7486        TCGA-HW-7487 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HW-7489        TCGA-HW-7490        TCGA-HW-7491        TCGA-HW-7493 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HW-7495        TCGA-HW-8319        TCGA-HW-8320        TCGA-HW-8321 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HW-8322        TCGA-HW-A5KJ        TCGA-HW-A5KK        TCGA-HW-A5KM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IK-7675        TCGA-IK-8125        TCGA-P5-A5ET        TCGA-P5-A5EU 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-P5-A5EV        TCGA-P5-A5EW        TCGA-P5-A5EX        TCGA-P5-A5EY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-P5-A5EZ        TCGA-P5-A5F0        TCGA-P5-A5F1        TCGA-P5-A5F2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-P5-A5F4        TCGA-P5-A5F6 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D3V7, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           2                92
  CLUS_2           1                77
  CLUS_3           0                97
D3V8, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           1                35
  CLUS_2           2               139
  CLUS_3           0                92
D3V9, multiclass
D3V10, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           0                14
  CLUS_2           3               142
  CLUS_3           0               109
D3V11, multiclass
D3V12, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           1                41
  CLUS_2           1               104
  CLUS_3           1               120

Clustering(4) Variable = 3q gain
D4V1, multiclass
[1] "Remove cluster labels:" "3Q GAIN CNV"           
clus
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DH-5144        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
D4V2, multiclass
[1] "Remove cluster labels:" "3Q GAIN CNV"           
clus
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DH-5144        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
D4V3, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           0                52
  CLUS_2           2                55
  CLUS_3           1                53
  CLUS_4           0               106
D4V4, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           1               121
  CLUS_2           2                40
  CLUS_3           0                66
  CLUS_4           0                34
D4V5, multiclass
[1] "Remove cluster labels:" "3Q GAIN CNV"           
clus
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                2               254 
       TCGA-CS-4938        TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CS-5390        TCGA-CS-5393        TCGA-CS-5394        TCGA-CS-5396 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CS-5397        TCGA-CS-6186        TCGA-CS-6188        TCGA-CS-6665 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CS-6666        TCGA-CS-6668        TCGA-CS-6669        TCGA-CS-6670 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DB-5270        TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DB-5276        TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5279 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DB-5280        TCGA-DB-5281        TCGA-DB-A4X9        TCGA-DB-A4XA 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DB-A4XB        TCGA-DB-A4XC        TCGA-DB-A4XD        TCGA-DB-A4XE 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DB-A4XF        TCGA-DB-A4XG        TCGA-DB-A4XH        TCGA-DH-5140 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-5847        TCGA-DU-5849        TCGA-DU-5851        TCGA-DU-5852 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-5853        TCGA-DU-5854        TCGA-DU-5855        TCGA-DU-5870 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-5871        TCGA-DU-5872        TCGA-DU-5874        TCGA-DU-6392 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-6393        TCGA-DU-6394        TCGA-DU-6395        TCGA-DU-6396 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-6397        TCGA-DU-6399        TCGA-DU-6400        TCGA-DU-6401 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-6402        TCGA-DU-6403        TCGA-DU-6404        TCGA-DU-6405 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-6406        TCGA-DU-6407        TCGA-DU-6408        TCGA-DU-6410 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-6542        TCGA-DU-7006        TCGA-DU-7007        TCGA-DU-7008 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-7009        TCGA-DU-7010        TCGA-DU-7011        TCGA-DU-7012 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-7014        TCGA-DU-7015        TCGA-DU-7018        TCGA-DU-7019 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-7290        TCGA-DU-7292        TCGA-DU-7294        TCGA-DU-7298 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-7300        TCGA-DU-7301        TCGA-DU-7302        TCGA-DU-7304 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-7306        TCGA-DU-7309        TCGA-DU-8158        TCGA-DU-8161 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-8162        TCGA-DU-8163        TCGA-DU-8164        TCGA-DU-8165 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-8166        TCGA-DU-8167        TCGA-DU-8168        TCGA-DU-A5TP 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-A5TR        TCGA-DU-A5TS        TCGA-DU-A5TT        TCGA-DU-A5TU 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-A5TW        TCGA-DU-A5TY        TCGA-E1-5302        TCGA-E1-5303 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-E1-5305        TCGA-E1-5307        TCGA-E1-5311        TCGA-E1-5318 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-E1-5319        TCGA-E1-5322        TCGA-EZ-7264        TCGA-FG-5962 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FG-5963        TCGA-FG-5964        TCGA-FG-5965        TCGA-FG-6688 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FG-6689        TCGA-FG-6690        TCGA-FG-6691        TCGA-FG-7634 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FG-7636        TCGA-FG-7638        TCGA-FG-7641        TCGA-FG-7643 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FG-8181        TCGA-FG-8182        TCGA-FG-8185        TCGA-FG-8186 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FG-8187        TCGA-FG-8188        TCGA-FG-8189        TCGA-FG-8191 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FG-A4MT        TCGA-FG-A4MU        TCGA-FG-A4MW        TCGA-FG-A4MX 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FG-A4MY        TCGA-FG-A60J        TCGA-HT-7467        TCGA-HT-7468 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7469        TCGA-HT-7470        TCGA-HT-7471        TCGA-HT-7472 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7473        TCGA-HT-7474        TCGA-HT-7475        TCGA-HT-7476 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7477        TCGA-HT-7478        TCGA-HT-7479        TCGA-HT-7480 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7481        TCGA-HT-7482        TCGA-HT-7483        TCGA-HT-7485 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7601        TCGA-HT-7602        TCGA-HT-7603        TCGA-HT-7604 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7605        TCGA-HT-7606        TCGA-HT-7607        TCGA-HT-7608 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7609        TCGA-HT-7610        TCGA-HT-7611        TCGA-HT-7616 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7620        TCGA-HT-7676        TCGA-HT-7677        TCGA-HT-7680 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7681        TCGA-HT-7684        TCGA-HT-7686        TCGA-HT-7687 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7688        TCGA-HT-7689        TCGA-HT-7690        TCGA-HT-7691 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7692        TCGA-HT-7693        TCGA-HT-7694        TCGA-HT-7695 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7854        TCGA-HT-7855        TCGA-HT-7856        TCGA-HT-7857 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7858        TCGA-HT-7860        TCGA-HT-7873        TCGA-HT-7874 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7875        TCGA-HT-7877        TCGA-HT-7879        TCGA-HT-7880 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7881        TCGA-HT-7882        TCGA-HT-7884        TCGA-HT-7902 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-8010        TCGA-HT-8011        TCGA-HT-8012        TCGA-HT-8013 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-8015        TCGA-HT-8018        TCGA-HT-8019        TCGA-HT-8104 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-8105        TCGA-HT-8106        TCGA-HT-8107        TCGA-HT-8109 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-8110        TCGA-HT-8111        TCGA-HT-8113        TCGA-HT-8114 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-8564        TCGA-HT-A4DV        TCGA-HT-A5R5        TCGA-HT-A5R7 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-A5R9        TCGA-HT-A5RB        TCGA-HW-7486        TCGA-HW-7487 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HW-7489        TCGA-HW-7490        TCGA-HW-7491        TCGA-HW-7493 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HW-7495        TCGA-HW-8319        TCGA-HW-8320        TCGA-HW-8321 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HW-8322        TCGA-HW-A5KJ        TCGA-HW-A5KK        TCGA-HW-A5KM 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-IK-7675        TCGA-IK-8125        TCGA-P5-A5ET        TCGA-P5-A5EU 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-P5-A5EV        TCGA-P5-A5EW        TCGA-P5-A5EX        TCGA-P5-A5EY 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-P5-A5EZ        TCGA-P5-A5F0        TCGA-P5-A5F1        TCGA-P5-A5F2 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-P5-A5F4        TCGA-P5-A5F6 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
D4V6, multiclass
[1] "Remove cluster labels:" "3Q GAIN CNV"           
clus
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                2               254 
       TCGA-CS-4938        TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CS-5390        TCGA-CS-5393        TCGA-CS-5394        TCGA-CS-5396 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CS-5397        TCGA-CS-6186        TCGA-CS-6188        TCGA-CS-6665 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CS-6666        TCGA-CS-6668        TCGA-CS-6669        TCGA-CS-6670 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DB-5270        TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DB-5276        TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5279 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DB-5280        TCGA-DB-5281        TCGA-DB-A4X9        TCGA-DB-A4XA 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DB-A4XB        TCGA-DB-A4XC        TCGA-DB-A4XD        TCGA-DB-A4XE 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DB-A4XF        TCGA-DB-A4XG        TCGA-DB-A4XH        TCGA-DH-5140 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-5847        TCGA-DU-5849        TCGA-DU-5851        TCGA-DU-5852 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-5853        TCGA-DU-5854        TCGA-DU-5855        TCGA-DU-5870 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-5871        TCGA-DU-5872        TCGA-DU-5874        TCGA-DU-6392 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-6393        TCGA-DU-6394        TCGA-DU-6395        TCGA-DU-6396 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-6397        TCGA-DU-6399        TCGA-DU-6400        TCGA-DU-6401 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-6402        TCGA-DU-6403        TCGA-DU-6404        TCGA-DU-6405 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-6406        TCGA-DU-6407        TCGA-DU-6408        TCGA-DU-6410 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-6542        TCGA-DU-7006        TCGA-DU-7007        TCGA-DU-7008 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-7009        TCGA-DU-7010        TCGA-DU-7011        TCGA-DU-7012 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-7014        TCGA-DU-7015        TCGA-DU-7018        TCGA-DU-7019 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-7290        TCGA-DU-7292        TCGA-DU-7294        TCGA-DU-7298 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-7300        TCGA-DU-7301        TCGA-DU-7302        TCGA-DU-7304 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-7306        TCGA-DU-7309        TCGA-DU-8158        TCGA-DU-8161 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-8162        TCGA-DU-8163        TCGA-DU-8164        TCGA-DU-8165 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-8166        TCGA-DU-8167        TCGA-DU-8168        TCGA-DU-A5TP 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-A5TR        TCGA-DU-A5TS        TCGA-DU-A5TT        TCGA-DU-A5TU 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DU-A5TW        TCGA-DU-A5TY        TCGA-E1-5302        TCGA-E1-5303 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-E1-5305        TCGA-E1-5307        TCGA-E1-5311        TCGA-E1-5318 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-E1-5319        TCGA-E1-5322        TCGA-EZ-7264        TCGA-FG-5962 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FG-5963        TCGA-FG-5964        TCGA-FG-5965        TCGA-FG-6688 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FG-6689        TCGA-FG-6690        TCGA-FG-6691        TCGA-FG-7634 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FG-7636        TCGA-FG-7638        TCGA-FG-7641        TCGA-FG-7643 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FG-8181        TCGA-FG-8182        TCGA-FG-8185        TCGA-FG-8186 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FG-8187        TCGA-FG-8188        TCGA-FG-8189        TCGA-FG-8191 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FG-A4MT        TCGA-FG-A4MU        TCGA-FG-A4MW        TCGA-FG-A4MX 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FG-A4MY        TCGA-FG-A60J        TCGA-HT-7467        TCGA-HT-7468 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7469        TCGA-HT-7470        TCGA-HT-7471        TCGA-HT-7472 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7473        TCGA-HT-7474        TCGA-HT-7475        TCGA-HT-7476 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7477        TCGA-HT-7478        TCGA-HT-7479        TCGA-HT-7480 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7481        TCGA-HT-7482        TCGA-HT-7483        TCGA-HT-7485 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7601        TCGA-HT-7602        TCGA-HT-7603        TCGA-HT-7604 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7605        TCGA-HT-7606        TCGA-HT-7607        TCGA-HT-7608 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7609        TCGA-HT-7610        TCGA-HT-7611        TCGA-HT-7616 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7620        TCGA-HT-7676        TCGA-HT-7677        TCGA-HT-7680 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7681        TCGA-HT-7684        TCGA-HT-7686        TCGA-HT-7687 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7688        TCGA-HT-7689        TCGA-HT-7690        TCGA-HT-7691 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7692        TCGA-HT-7693        TCGA-HT-7694        TCGA-HT-7695 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7854        TCGA-HT-7855        TCGA-HT-7856        TCGA-HT-7857 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7858        TCGA-HT-7860        TCGA-HT-7873        TCGA-HT-7874 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7875        TCGA-HT-7877        TCGA-HT-7879        TCGA-HT-7880 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-7881        TCGA-HT-7882        TCGA-HT-7884        TCGA-HT-7902 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-8010        TCGA-HT-8011        TCGA-HT-8012        TCGA-HT-8013 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-8015        TCGA-HT-8018        TCGA-HT-8019        TCGA-HT-8104 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-8105        TCGA-HT-8106        TCGA-HT-8107        TCGA-HT-8109 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-8110        TCGA-HT-8111        TCGA-HT-8113        TCGA-HT-8114 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-8564        TCGA-HT-A4DV        TCGA-HT-A5R5        TCGA-HT-A5R7 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HT-A5R9        TCGA-HT-A5RB        TCGA-HW-7486        TCGA-HW-7487 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HW-7489        TCGA-HW-7490        TCGA-HW-7491        TCGA-HW-7493 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HW-7495        TCGA-HW-8319        TCGA-HW-8320        TCGA-HW-8321 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HW-8322        TCGA-HW-A5KJ        TCGA-HW-A5KK        TCGA-HW-A5KM 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-IK-7675        TCGA-IK-8125        TCGA-P5-A5ET        TCGA-P5-A5EU 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-P5-A5EV        TCGA-P5-A5EW        TCGA-P5-A5EX        TCGA-P5-A5EY 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-P5-A5EZ        TCGA-P5-A5F0        TCGA-P5-A5F1        TCGA-P5-A5F2 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-P5-A5F4        TCGA-P5-A5F6 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
D4V7, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           3                91
  CLUS_2           0                78
  CLUS_3           0                97
D4V8, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           0                36
  CLUS_2           3               138
  CLUS_3           0                92
D4V9, multiclass
D4V10, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           0                14
  CLUS_2           3               142
  CLUS_3           0               109
D4V11, multiclass
D4V12, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           2                40
  CLUS_2           1               104
  CLUS_3           0               121

Clustering(5) Variable = 4p gain
D5V1, multiclass
D5V2, multiclass
D5V3, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           1                51
  CLUS_2           0                57
  CLUS_3           3                51
  CLUS_4           0               106
D5V4, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           4               118
  CLUS_2           0                42
  CLUS_3           0                66
  CLUS_4           0                34
D5V5, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           1                51
  CLUS_2           2                60
  CLUS_3           0                68
  CLUS_4           1                73
D5V6, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           2               127
  CLUS_3           2               117
D5V7, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           3                91
  CLUS_2           0                78
  CLUS_3           1                96
D5V8, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           0                36
  CLUS_2           3               138
  CLUS_3           1                91
D5V9, multiclass
D5V10, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           1                13
  CLUS_2           1               144
  CLUS_3           2               107
D5V11, multiclass
D5V12, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           1                41
  CLUS_2           2               103
  CLUS_3           1               120

Clustering(6) Variable = 6p gain
D6V1, multiclass
[1] "Remove cluster labels:" "6P GAIN CNV"           
clus
      6P GAIN CNV 6P GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DH-5144        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
D6V2, multiclass
[1] "Remove cluster labels:" "6P GAIN CNV"           
clus
      6P GAIN CNV 6P GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DH-5144        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
D6V3, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           0                52
  CLUS_2           0                57
  CLUS_3           3                51
  CLUS_4           0               106
D6V4, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           3               119
  CLUS_2           0                42
  CLUS_3           0                66
  CLUS_4           0                34
D6V5, multiclass
[1] "Remove cluster labels:" "6P GAIN CNV"           
clus
      6P GAIN CNV 6P GAIN WILD-TYPE 
                2               254 
       TCGA-CS-4938        TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CS-5390        TCGA-CS-5393        TCGA-CS-5394        TCGA-CS-5396 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CS-5397        TCGA-CS-6186        TCGA-CS-6188        TCGA-CS-6666 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CS-6668        TCGA-CS-6669        TCGA-CS-6670        TCGA-DB-5270 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5279        TCGA-DB-5280 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DB-5281        TCGA-DB-A4X9        TCGA-DB-A4XA        TCGA-DB-A4XB 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DB-A4XC        TCGA-DB-A4XD        TCGA-DB-A4XE        TCGA-DB-A4XF 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DB-A4XG        TCGA-DB-A4XH        TCGA-DH-5140        TCGA-DH-5141 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144        TCGA-DU-5847 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-5849        TCGA-DU-5851        TCGA-DU-5852        TCGA-DU-5853 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-5854        TCGA-DU-5855        TCGA-DU-5870        TCGA-DU-5871 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-5872        TCGA-DU-5874        TCGA-DU-6392        TCGA-DU-6393 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-6394        TCGA-DU-6395        TCGA-DU-6396        TCGA-DU-6397 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-6399        TCGA-DU-6400        TCGA-DU-6401        TCGA-DU-6402 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-6403        TCGA-DU-6404        TCGA-DU-6405        TCGA-DU-6406 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-6407        TCGA-DU-6408        TCGA-DU-6410        TCGA-DU-6542 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-7006        TCGA-DU-7007        TCGA-DU-7008        TCGA-DU-7009 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-7010        TCGA-DU-7011        TCGA-DU-7012        TCGA-DU-7013 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-7014        TCGA-DU-7015        TCGA-DU-7018        TCGA-DU-7019 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-7290        TCGA-DU-7292        TCGA-DU-7294        TCGA-DU-7298 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-7300        TCGA-DU-7301        TCGA-DU-7302        TCGA-DU-7304 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-7306        TCGA-DU-7309        TCGA-DU-8158        TCGA-DU-8161 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-8162        TCGA-DU-8163        TCGA-DU-8164        TCGA-DU-8165 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-8166        TCGA-DU-8167        TCGA-DU-8168        TCGA-DU-A5TP 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-A5TR        TCGA-DU-A5TS        TCGA-DU-A5TT        TCGA-DU-A5TU 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-A5TW        TCGA-DU-A5TY        TCGA-E1-5302        TCGA-E1-5303 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-E1-5305        TCGA-E1-5307        TCGA-E1-5311        TCGA-E1-5318 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-E1-5319        TCGA-E1-5322        TCGA-EZ-7264        TCGA-FG-5962 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FG-5963        TCGA-FG-5964        TCGA-FG-5965        TCGA-FG-6688 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FG-6689        TCGA-FG-6690        TCGA-FG-6691        TCGA-FG-7634 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FG-7636        TCGA-FG-7638        TCGA-FG-7641        TCGA-FG-7643 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FG-8181        TCGA-FG-8182        TCGA-FG-8185        TCGA-FG-8186 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FG-8187        TCGA-FG-8188        TCGA-FG-8189        TCGA-FG-8191 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FG-A4MT        TCGA-FG-A4MU        TCGA-FG-A4MW        TCGA-FG-A4MX 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FG-A4MY        TCGA-FG-A60J        TCGA-HT-7467        TCGA-HT-7468 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7469        TCGA-HT-7470        TCGA-HT-7471        TCGA-HT-7472 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7473        TCGA-HT-7474        TCGA-HT-7475        TCGA-HT-7476 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7477        TCGA-HT-7478        TCGA-HT-7479        TCGA-HT-7480 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7481        TCGA-HT-7482        TCGA-HT-7483        TCGA-HT-7485 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7601        TCGA-HT-7602        TCGA-HT-7603        TCGA-HT-7604 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7605        TCGA-HT-7606        TCGA-HT-7607        TCGA-HT-7608 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7609        TCGA-HT-7610        TCGA-HT-7611        TCGA-HT-7616 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7620        TCGA-HT-7676        TCGA-HT-7677        TCGA-HT-7680 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7681        TCGA-HT-7684        TCGA-HT-7686        TCGA-HT-7687 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7688        TCGA-HT-7689        TCGA-HT-7690        TCGA-HT-7691 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7692        TCGA-HT-7693        TCGA-HT-7694        TCGA-HT-7695 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7854        TCGA-HT-7855        TCGA-HT-7856        TCGA-HT-7857 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7858        TCGA-HT-7860        TCGA-HT-7873        TCGA-HT-7874 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7875        TCGA-HT-7877        TCGA-HT-7879        TCGA-HT-7880 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7881        TCGA-HT-7882        TCGA-HT-7884        TCGA-HT-7902 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-8010        TCGA-HT-8011        TCGA-HT-8012        TCGA-HT-8013 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-8015        TCGA-HT-8018        TCGA-HT-8019        TCGA-HT-8104 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-8105        TCGA-HT-8106        TCGA-HT-8107        TCGA-HT-8109 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-8110        TCGA-HT-8111        TCGA-HT-8113        TCGA-HT-8114 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-8564        TCGA-HT-A4DV        TCGA-HT-A5R5        TCGA-HT-A5R7 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-A5R9        TCGA-HT-A5RB        TCGA-HW-7486        TCGA-HW-7487 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HW-7489        TCGA-HW-7490        TCGA-HW-7491        TCGA-HW-7493 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HW-7495        TCGA-HW-8319        TCGA-HW-8320        TCGA-HW-8321 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HW-8322        TCGA-HW-A5KJ        TCGA-HW-A5KK        TCGA-HW-A5KM 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IK-7675        TCGA-IK-8125        TCGA-P5-A5ET        TCGA-P5-A5EU 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-P5-A5EV        TCGA-P5-A5EW        TCGA-P5-A5EX        TCGA-P5-A5EY 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-P5-A5EZ        TCGA-P5-A5F0        TCGA-P5-A5F1        TCGA-P5-A5F2 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-P5-A5F4        TCGA-P5-A5F6 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
D6V6, multiclass
[1] "Remove cluster labels:" "6P GAIN CNV"           
clus
      6P GAIN CNV 6P GAIN WILD-TYPE 
                2               254 
       TCGA-CS-4938        TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CS-5390        TCGA-CS-5393        TCGA-CS-5394        TCGA-CS-5396 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CS-5397        TCGA-CS-6186        TCGA-CS-6188        TCGA-CS-6666 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CS-6668        TCGA-CS-6669        TCGA-CS-6670        TCGA-DB-5270 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5279        TCGA-DB-5280 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DB-5281        TCGA-DB-A4X9        TCGA-DB-A4XA        TCGA-DB-A4XB 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DB-A4XC        TCGA-DB-A4XD        TCGA-DB-A4XE        TCGA-DB-A4XF 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DB-A4XG        TCGA-DB-A4XH        TCGA-DH-5140        TCGA-DH-5141 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144        TCGA-DU-5847 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-5849        TCGA-DU-5851        TCGA-DU-5852        TCGA-DU-5853 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-5854        TCGA-DU-5855        TCGA-DU-5870        TCGA-DU-5871 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-5872        TCGA-DU-5874        TCGA-DU-6392        TCGA-DU-6393 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-6394        TCGA-DU-6395        TCGA-DU-6396        TCGA-DU-6397 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-6399        TCGA-DU-6400        TCGA-DU-6401        TCGA-DU-6402 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-6403        TCGA-DU-6404        TCGA-DU-6405        TCGA-DU-6406 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-6407        TCGA-DU-6408        TCGA-DU-6410        TCGA-DU-6542 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-7006        TCGA-DU-7007        TCGA-DU-7008        TCGA-DU-7009 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-7010        TCGA-DU-7011        TCGA-DU-7012        TCGA-DU-7013 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-7014        TCGA-DU-7015        TCGA-DU-7018        TCGA-DU-7019 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-7290        TCGA-DU-7292        TCGA-DU-7294        TCGA-DU-7298 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-7300        TCGA-DU-7301        TCGA-DU-7302        TCGA-DU-7304 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-7306        TCGA-DU-7309        TCGA-DU-8158        TCGA-DU-8161 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-8162        TCGA-DU-8163        TCGA-DU-8164        TCGA-DU-8165 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-8166        TCGA-DU-8167        TCGA-DU-8168        TCGA-DU-A5TP 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-A5TR        TCGA-DU-A5TS        TCGA-DU-A5TT        TCGA-DU-A5TU 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DU-A5TW        TCGA-DU-A5TY        TCGA-E1-5302        TCGA-E1-5303 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-E1-5305        TCGA-E1-5307        TCGA-E1-5311        TCGA-E1-5318 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-E1-5319        TCGA-E1-5322        TCGA-EZ-7264        TCGA-FG-5962 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FG-5963        TCGA-FG-5964        TCGA-FG-5965        TCGA-FG-6688 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FG-6689        TCGA-FG-6690        TCGA-FG-6691        TCGA-FG-7634 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FG-7636        TCGA-FG-7638        TCGA-FG-7641        TCGA-FG-7643 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FG-8181        TCGA-FG-8182        TCGA-FG-8185        TCGA-FG-8186 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FG-8187        TCGA-FG-8188        TCGA-FG-8189        TCGA-FG-8191 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FG-A4MT        TCGA-FG-A4MU        TCGA-FG-A4MW        TCGA-FG-A4MX 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FG-A4MY        TCGA-FG-A60J        TCGA-HT-7467        TCGA-HT-7468 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7469        TCGA-HT-7470        TCGA-HT-7471        TCGA-HT-7472 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7473        TCGA-HT-7474        TCGA-HT-7475        TCGA-HT-7476 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7477        TCGA-HT-7478        TCGA-HT-7479        TCGA-HT-7480 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7481        TCGA-HT-7482        TCGA-HT-7483        TCGA-HT-7485 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7601        TCGA-HT-7602        TCGA-HT-7603        TCGA-HT-7604 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7605        TCGA-HT-7606        TCGA-HT-7607        TCGA-HT-7608 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7609        TCGA-HT-7610        TCGA-HT-7611        TCGA-HT-7616 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7620        TCGA-HT-7676        TCGA-HT-7677        TCGA-HT-7680 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7681        TCGA-HT-7684        TCGA-HT-7686        TCGA-HT-7687 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7688        TCGA-HT-7689        TCGA-HT-7690        TCGA-HT-7691 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7692        TCGA-HT-7693        TCGA-HT-7694        TCGA-HT-7695 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7854        TCGA-HT-7855        TCGA-HT-7856        TCGA-HT-7857 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7858        TCGA-HT-7860        TCGA-HT-7873        TCGA-HT-7874 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7875        TCGA-HT-7877        TCGA-HT-7879        TCGA-HT-7880 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-7881        TCGA-HT-7882        TCGA-HT-7884        TCGA-HT-7902 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-8010        TCGA-HT-8011        TCGA-HT-8012        TCGA-HT-8013 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-8015        TCGA-HT-8018        TCGA-HT-8019        TCGA-HT-8104 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-8105        TCGA-HT-8106        TCGA-HT-8107        TCGA-HT-8109 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-8110        TCGA-HT-8111        TCGA-HT-8113        TCGA-HT-8114 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-8564        TCGA-HT-A4DV        TCGA-HT-A5R5        TCGA-HT-A5R7 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HT-A5R9        TCGA-HT-A5RB        TCGA-HW-7486        TCGA-HW-7487 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HW-7489        TCGA-HW-7490        TCGA-HW-7491        TCGA-HW-7493 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HW-7495        TCGA-HW-8319        TCGA-HW-8320        TCGA-HW-8321 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HW-8322        TCGA-HW-A5KJ        TCGA-HW-A5KK        TCGA-HW-A5KM 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IK-7675        TCGA-IK-8125        TCGA-P5-A5ET        TCGA-P5-A5EU 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-P5-A5EV        TCGA-P5-A5EW        TCGA-P5-A5EX        TCGA-P5-A5EY 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-P5-A5EZ        TCGA-P5-A5F0        TCGA-P5-A5F1        TCGA-P5-A5F2 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-P5-A5F4        TCGA-P5-A5F6 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
D6V7, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           3                91
  CLUS_2           0                78
  CLUS_3           0                97
D6V8, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           0                36
  CLUS_2           3               138
  CLUS_3           0                92
D6V9, multiclass
D6V10, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           1                13
  CLUS_2           2               143
  CLUS_3           0               109
D6V11, multiclass
D6V12, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           1                41
  CLUS_2           2               103
  CLUS_3           0               121

Clustering(7) Variable = 7p gain
D7V1, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           1                 8
  CLUS_2           0                10
  CLUS_3           2                 6
D7V2, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           0                 7
  CLUS_2           1                 5
  CLUS_3           2                 8
  CLUS_4           0                 4
D7V3, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           2                50
  CLUS_2          41                16
  CLUS_3           4                50
  CLUS_4           3               103
D7V4, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          16               106
  CLUS_2          27                15
  CLUS_3           4                62
  CLUS_4           2                32
D7V5, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           9                43
  CLUS_2          23                39
  CLUS_3           8                60
  CLUS_4           5                69
D7V6, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           0                 8
  CLUS_2          32                97
  CLUS_3          13               106
D7V7, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          33                61
  CLUS_2          11                67
  CLUS_3           6                91
D7V8, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           3                33
  CLUS_2          40               101
  CLUS_3           7                85
D7V9, multiclass
D7V10, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           9                 5
  CLUS_2          33               112
  CLUS_3           8               101
D7V11, multiclass
D7V12, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          25                17
  CLUS_2          16                89
  CLUS_3           9               112

Clustering(8) Variable = 7q gain
D8V1, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           2                 7
  CLUS_2           0                10
  CLUS_3           2                 6
D8V2, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           0                 7
  CLUS_2           1                 5
  CLUS_3           3                 7
  CLUS_4           0                 4
D8V3, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           5                47
  CLUS_2          46                11
  CLUS_3           6                48
  CLUS_4          11                95
D8V4, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          25                97
  CLUS_2          30                12
  CLUS_3           9                57
  CLUS_4           3                31
D8V5, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          14                38
  CLUS_2          25                37
  CLUS_3          10                58
  CLUS_4          12                62
D8V6, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           0                 8
  CLUS_2          38                91
  CLUS_3          23                96
D8V7, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          39                55
  CLUS_2          17                61
  CLUS_3          12                85
D8V8, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           6                30
  CLUS_2          50                91
  CLUS_3          12                80
D8V9, multiclass
D8V10, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           9                 5
  CLUS_2          40               105
  CLUS_3          19                90
D8V11, multiclass
D8V12, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          27                15
  CLUS_2          21                84
  CLUS_3          20               101

Clustering(9) Variable = 8p gain
D9V1, multiclass
[1] "Remove cluster labels:" "8P GAIN CNV"           
clus
      8P GAIN CNV 8P GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DH-5140 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
D9V2, multiclass
[1] "Remove cluster labels:" "8P GAIN CNV"           
clus
      8P GAIN CNV 8P GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DH-5140 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
D9V3, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           6                46
  CLUS_2           4                53
  CLUS_3           7                47
  CLUS_4           0               106
D9V4, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          13               109
  CLUS_2           2                40
  CLUS_3           1                65
  CLUS_4           1                33
D9V5, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           5                47
  CLUS_2           5                57
  CLUS_3           6                62
  CLUS_4           1                73
D9V6, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           0                 8
  CLUS_2          10               119
  CLUS_3           7               112
D9V7, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           7                87
  CLUS_2           7                71
  CLUS_3           3                94
D9V8, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           1                35
  CLUS_2          12               129
  CLUS_3           4                88
D9V9, multiclass
D9V10, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           1                13
  CLUS_2          10               135
  CLUS_3           6               103
D9V11, multiclass
D9V12, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           3                39
  CLUS_2          10                95
  CLUS_3           4               117

Clustering(10) Variable = 8q gain
D10V1, multiclass
[1] "Remove cluster labels:" "8Q GAIN CNV"           
clus
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DH-5140        TCGA-DH-5141 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144        TCGA-E1-5302 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-E1-5322 
"8Q GAIN WILD-TYPE" 
D10V2, multiclass
[1] "Remove cluster labels:" "8Q GAIN CNV"           
clus
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DH-5140        TCGA-DH-5141 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144        TCGA-E1-5302 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-E1-5322 
"8Q GAIN WILD-TYPE" 
D10V3, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           8                44
  CLUS_2           6                51
  CLUS_3           8                46
  CLUS_4           0               106
D10V4, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          17               105
  CLUS_2           2                40
  CLUS_3           1                65
  CLUS_4           2                32
D10V5, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           7                45
  CLUS_2           6                56
  CLUS_3           8                60
  CLUS_4           1                73
D10V6, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           0                 8
  CLUS_2          14               115
  CLUS_3           8               111
D10V7, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           8                86
  CLUS_2          10                68
  CLUS_3           4                93
D10V8, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           1                35
  CLUS_2          17               124
  CLUS_3           4                88
D10V9, multiclass
D10V10, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           1                13
  CLUS_2          14               131
  CLUS_3           7               102
D10V11, multiclass
D10V12, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           3                39
  CLUS_2          15                90
  CLUS_3           4               117

Clustering(11) Variable = 9p gain
D11V1, multiclass
D11V2, multiclass
D11V3, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           2                50
  CLUS_2           1                56
  CLUS_3           3                51
  CLUS_4           0               106
D11V4, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           3               119
  CLUS_2           2                40
  CLUS_3           0                66
  CLUS_4           1                33
D11V5, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           1                51
  CLUS_2           3                59
  CLUS_3           0                68
  CLUS_4           2                72
D11V6, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           2               127
  CLUS_3           4               115
D11V7, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           4                90
  CLUS_2           1                77
  CLUS_3           1                96
D11V8, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           0                36
  CLUS_2           4               137
  CLUS_3           2                90
D11V9, multiclass
D11V10, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           1                13
  CLUS_2           3               142
  CLUS_3           2               107
D11V11, multiclass
D11V12, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           2                40
  CLUS_2           1               104
  CLUS_3           3               118

Clustering(12) Variable = 9q gain
D12V1, multiclass
D12V2, multiclass
D12V3, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           2                50
  CLUS_2           2                55
  CLUS_3           5                49
  CLUS_4           0               106
D12V4, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           6               116
  CLUS_2           3                39
  CLUS_3           0                66
  CLUS_4           0                34
D12V5, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           2                50
  CLUS_2           5                57
  CLUS_3           1                67
  CLUS_4           1                73
D12V6, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           5               124
  CLUS_3           4               115
D12V7, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           7                87
  CLUS_2           1                77
  CLUS_3           1                96
D12V8, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           0                36
  CLUS_2           7               134
  CLUS_3           2                90
D12V9, multiclass
D12V10, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           1                13
  CLUS_2           5               140
  CLUS_3           3               106
D12V11, multiclass
D12V12, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           3                39
  CLUS_2           3               102
  CLUS_3           3               118

Clustering(13) Variable = 10p gain
D13V1, multiclass
[1] "Remove cluster labels:" "10P GAIN CNV"          
clus
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-E1-5318 
"10P GAIN WILD-TYPE" 
D13V2, multiclass
[1] "Remove cluster labels:" "10P GAIN CNV"          
clus
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-E1-5318 
"10P GAIN WILD-TYPE" 
D13V3, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           12                 40
  CLUS_2            3                 54
  CLUS_3            7                 47
  CLUS_4            2                104
D13V4, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           23                 99
  CLUS_2            0                 42
  CLUS_3            0                 66
  CLUS_4            1                 33
D13V5, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            8                 44
  CLUS_2            4                 58
  CLUS_3            7                 61
  CLUS_4            3                 71
D13V6, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            0                  8
  CLUS_2           14                115
  CLUS_3            8                111
D13V7, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            9                 85
  CLUS_2            7                 71
  CLUS_3            8                 89
D13V8, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            0                 36
  CLUS_2           17                124
  CLUS_3            7                 85
D13V9, multiclass
D13V10, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            0                 14
  CLUS_2           15                130
  CLUS_3            9                100
D13V11, multiclass
D13V12, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            1                 41
  CLUS_2           12                 93
  CLUS_3           11                110

Clustering(14) Variable = 11p gain
D14V1, multiclass
[1] "Remove cluster labels:" "11P GAIN CNV"          
clus
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D14V2, multiclass
[1] "Remove cluster labels:" "11P GAIN CNV"          
clus
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D14V3, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            1                 51
  CLUS_2            2                 55
  CLUS_3            3                 51
  CLUS_4            5                101
D14V4, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            5                117
  CLUS_2            0                 42
  CLUS_3            5                 61
  CLUS_4            1                 33
D14V5, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            0                 52
  CLUS_2            3                 59
  CLUS_3            6                 62
  CLUS_4            2                 72
D14V6, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            7                122
  CLUS_3            4                115
D14V7, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            2                 92
  CLUS_2            6                 72
  CLUS_3            3                 94
D14V8, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            5                 31
  CLUS_2            3                138
  CLUS_3            3                 89
D14V9, multiclass
D14V10, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            7                138
  CLUS_3            4                105
D14V11, multiclass
D14V12, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            0                 42
  CLUS_2            7                 98
  CLUS_3            4                117

Clustering(15) Variable = 11q gain
D15V1, multiclass
[1] "Remove cluster labels:" "11Q GAIN CNV"          
clus
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D15V2, multiclass
[1] "Remove cluster labels:" "11Q GAIN CNV"          
clus
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D15V3, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            5                 47
  CLUS_2            2                 55
  CLUS_3            1                 53
  CLUS_4            7                 99
D15V4, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            9                113
  CLUS_2            0                 42
  CLUS_3            5                 61
  CLUS_4            1                 33
D15V5, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            3                 49
  CLUS_2            1                 61
  CLUS_3            9                 59
  CLUS_4            2                 72
D15V6, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            0                  8
  CLUS_2           11                118
  CLUS_3            4                115
D15V7, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            4                 90
  CLUS_2            7                 71
  CLUS_3            4                 93
D15V8, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            5                 31
  CLUS_2            5                136
  CLUS_3            5                 87
D15V9, multiclass
D15V10, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            0                 14
  CLUS_2           10                135
  CLUS_3            5                104
D15V11, multiclass
D15V12, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            0                 42
  CLUS_2           10                 95
  CLUS_3            5                116

Clustering(16) Variable = 12p gain
D16V1, multiclass
[1] "Remove cluster labels:" "12P GAIN CNV"          
clus
      12P GAIN CNV 12P GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5274 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DB-5276         TCGA-DB-5277         TCGA-DB-5278 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DB-5280         TCGA-DB-5281         TCGA-DH-5140 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DH-5141         TCGA-DH-5142         TCGA-DH-5143 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DH-5144         TCGA-E1-5302         TCGA-E1-5303 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-E1-5304         TCGA-E1-5311         TCGA-E1-5318 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-E1-5322 
"12P GAIN WILD-TYPE" 
D16V2, multiclass
[1] "Remove cluster labels:" "12P GAIN CNV"          
clus
      12P GAIN CNV 12P GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5274 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DB-5276         TCGA-DB-5277         TCGA-DB-5278 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DB-5280         TCGA-DB-5281         TCGA-DH-5140 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DH-5141         TCGA-DH-5142         TCGA-DH-5143 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DH-5144         TCGA-E1-5302         TCGA-E1-5303 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-E1-5304         TCGA-E1-5311         TCGA-E1-5318 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-E1-5322 
"12P GAIN WILD-TYPE" 
D16V3, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            7                 45
  CLUS_2            3                 54
  CLUS_3            3                 51
  CLUS_4            0                106
D16V4, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            9                113
  CLUS_2            1                 41
  CLUS_3            1                 65
  CLUS_4            2                 32
D16V5, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            4                 48
  CLUS_2            4                 58
  CLUS_3            3                 65
  CLUS_4            2                 72
D16V6, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            7                122
  CLUS_3            6                113
D16V7, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            5                 89
  CLUS_2            7                 71
  CLUS_3            1                 96
D16V8, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            1                 35
  CLUS_2           11                130
  CLUS_3            1                 91
D16V9, multiclass
D16V10, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            0                 14
  CLUS_2           11                134
  CLUS_3            2                107
D16V11, multiclass
D16V12, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            2                 40
  CLUS_2            9                 96
  CLUS_3            2                119

Clustering(17) Variable = 12q gain
D17V1, multiclass
D17V2, multiclass
D17V3, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            1                 51
  CLUS_2            2                 55
  CLUS_3            2                 52
  CLUS_4            0                106
D17V4, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            3                119
  CLUS_2            1                 41
  CLUS_3            1                 65
  CLUS_4            0                 34
D17V5, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            2                 50
  CLUS_2            2                 60
  CLUS_3            1                 67
  CLUS_4            0                 74
D17V6, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            2                127
  CLUS_3            3                116
D17V7, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            2                 92
  CLUS_2            3                 75
  CLUS_3            0                 97
D17V8, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            1                 35
  CLUS_2            4                137
  CLUS_3            0                 92
D17V9, multiclass
D17V10, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            5                140
  CLUS_3            0                109
D17V11, multiclass
D17V12, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            2                 40
  CLUS_2            3                102
  CLUS_3            0                121

Clustering(18) Variable = 18p gain
D18V1, multiclass
[1] "Remove cluster labels:" "18P GAIN CNV"          
clus
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
D18V2, multiclass
[1] "Remove cluster labels:" "18P GAIN CNV"          
clus
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
D18V3, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            2                 50
  CLUS_2            1                 56
  CLUS_3            3                 51
  CLUS_4            1                105
D18V4, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            4                118
  CLUS_2            2                 40
  CLUS_3            1                 65
  CLUS_4            0                 34
D18V5, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            2                 50
  CLUS_2            4                 58
  CLUS_3            0                 68
  CLUS_4            1                 73
D18V6, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            3                126
  CLUS_3            4                115
D18V7, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            5                 89
  CLUS_2            1                 77
  CLUS_3            1                 96
D18V8, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            0                 36
  CLUS_2            6                135
  CLUS_3            1                 91
D18V9, multiclass
D18V10, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            5                140
  CLUS_3            2                107
D18V11, multiclass
D18V12, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            1                 41
  CLUS_2            4                101
  CLUS_3            2                119

Clustering(19) Variable = 18q gain
D19V1, multiclass
D19V2, multiclass
D19V3, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            1                 51
  CLUS_2            1                 56
  CLUS_3            2                 52
  CLUS_4            0                106
D19V4, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            2                120
  CLUS_2            2                 40
  CLUS_3            0                 66
  CLUS_4            0                 34
D19V5, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            1                 51
  CLUS_2            3                 59
  CLUS_3            0                 68
  CLUS_4            0                 74
D19V6, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            2                127
  CLUS_3            2                117
D19V7, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            4                 90
  CLUS_2            0                 78
  CLUS_3            0                 97
D19V8, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            0                 36
  CLUS_2            4                137
  CLUS_3            0                 92
D19V9, multiclass
D19V10, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            4                141
  CLUS_3            0                109
D19V11, multiclass
D19V12, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            1                 41
  CLUS_2            2                103
  CLUS_3            1                120

Clustering(20) Variable = 19p gain
D20V1, multiclass
[1] "Remove cluster labels:" "19P GAIN CNV"          
clus
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5396 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
D20V2, multiclass
[1] "Remove cluster labels:" "19P GAIN CNV"          
clus
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5396 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
D20V3, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            1                 51
  CLUS_2           14                 43
  CLUS_3            1                 53
  CLUS_4            1                105
D20V4, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            4                118
  CLUS_2           13                 29
  CLUS_3            0                 66
  CLUS_4            0                 34
D20V5, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            4                 48
  CLUS_2            6                 56
  CLUS_3            3                 65
  CLUS_4            0                 74
D20V6, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            0                  8
  CLUS_2           11                118
  CLUS_3            2                117
D20V7, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1           14                 80
  CLUS_2            2                 76
  CLUS_3            1                 96
D20V8, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            0                 36
  CLUS_2           17                124
  CLUS_3            0                 92
D20V9, multiclass
D20V10, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            4                 10
  CLUS_2           11                134
  CLUS_3            2                107
D20V11, multiclass
D20V12, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1           12                 30
  CLUS_2            4                101
  CLUS_3            1                120

Clustering(21) Variable = 19q gain
D21V1, multiclass
[1] "Remove cluster labels:" "19Q GAIN CNV"          
clus
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5396 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
D21V2, multiclass
[1] "Remove cluster labels:" "19Q GAIN CNV"          
clus
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5396 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
D21V3, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            0                 52
  CLUS_2           10                 47
  CLUS_3            1                 53
  CLUS_4            1                105
D21V4, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            2                120
  CLUS_2            9                 33
  CLUS_3            0                 66
  CLUS_4            0                 34
D21V5, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            3                 49
  CLUS_2            5                 57
  CLUS_3            1                 67
  CLUS_4            0                 74
D21V6, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            7                122
  CLUS_3            2                117
D21V7, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1           10                 84
  CLUS_2            1                 77
  CLUS_3            1                 96
D21V8, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            0                 36
  CLUS_2           12                129
  CLUS_3            0                 92
D21V9, multiclass
D21V10, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            3                 11
  CLUS_2            8                137
  CLUS_3            1                108
D21V11, multiclass
D21V12, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            9                 33
  CLUS_2            2                103
  CLUS_3            1                120

Clustering(22) Variable = 20p gain
D22V1, multiclass
[1] "Remove cluster labels:" "20P GAIN CNV"          
clus
      20P GAIN CNV 20P GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5396 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-E1-5322 
"20P GAIN WILD-TYPE" 
D22V2, multiclass
[1] "Remove cluster labels:" "20P GAIN CNV"          
clus
      20P GAIN CNV 20P GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5396 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-E1-5322 
"20P GAIN WILD-TYPE" 
D22V3, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            2                 50
  CLUS_2           13                 44
  CLUS_3            5                 49
  CLUS_4            0                106
D22V4, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            3                119
  CLUS_2           14                 28
  CLUS_3            1                 65
  CLUS_4            2                 32
D22V5, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            3                 49
  CLUS_2           11                 51
  CLUS_3            2                 66
  CLUS_4            2                 72
D22V6, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            0                  8
  CLUS_2           12                117
  CLUS_3            6                113
D22V7, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           15                 79
  CLUS_2            1                 77
  CLUS_3            4                 93
D22V8, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            1                 35
  CLUS_2           16                125
  CLUS_3            3                 89
D22V9, multiclass
D22V10, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            5                  9
  CLUS_2           11                134
  CLUS_3            4                105
D22V11, multiclass
D22V12, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           13                 29
  CLUS_2            5                100
  CLUS_3            2                119

Clustering(23) Variable = 20q gain
D23V1, multiclass
[1] "Remove cluster labels:" "20Q GAIN CNV"          
clus
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5396 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-E1-5322 
"20Q GAIN WILD-TYPE" 
D23V2, multiclass
[1] "Remove cluster labels:" "20Q GAIN CNV"          
clus
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5396 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-E1-5322 
"20Q GAIN WILD-TYPE" 
D23V3, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            2                 50
  CLUS_2           13                 44
  CLUS_3            5                 49
  CLUS_4            0                106
D23V4, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            5                117
  CLUS_2           14                 28
  CLUS_3            1                 65
  CLUS_4            0                 34
D23V5, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            4                 48
  CLUS_2           11                 51
  CLUS_3            2                 66
  CLUS_4            0                 74
D23V6, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            0                  8
  CLUS_2           12                117
  CLUS_3            5                114
D23V7, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           17                 77
  CLUS_2            1                 77
  CLUS_3            2                 95
D23V8, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            1                 35
  CLUS_2           18                123
  CLUS_3            1                 91
D23V9, multiclass
D23V10, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            5                  9
  CLUS_2           13                132
  CLUS_3            2                107
D23V11, multiclass
D23V12, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           13                 29
  CLUS_2            7                 98
  CLUS_3            0                121

Clustering(24) Variable = 21q gain
D24V1, multiclass
D24V2, multiclass
D24V3, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            0                 52
  CLUS_2            4                 53
  CLUS_3            1                 53
  CLUS_4            1                105
D24V4, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            1                121
  CLUS_2            3                 39
  CLUS_3            2                 64
  CLUS_4            0                 34
D24V5, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            0                 52
  CLUS_2            3                 59
  CLUS_3            2                 66
  CLUS_4            0                 74
D24V6, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            4                125
  CLUS_3            1                118
D24V7, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            3                 91
  CLUS_2            3                 75
  CLUS_3            0                 97
D24V8, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            2                 34
  CLUS_2            4                137
  CLUS_3            0                 92
D24V9, multiclass
D24V10, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            5                140
  CLUS_3            1                108
D24V11, multiclass
D24V12, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            3                 39
  CLUS_2            2                103
  CLUS_3            1                120

Clustering(25) Variable = 1p loss
D25V1, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           0                 9
  CLUS_2           7                 3
  CLUS_3           2                 6
D25V2, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           7                 0
  CLUS_2           2                 4
  CLUS_3           0                10
  CLUS_4           0                 4
D25V3, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           0                52
  CLUS_2           0                57
  CLUS_3          12                42
  CLUS_4          65                41
D25V4, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           1               121
  CLUS_2           0                42
  CLUS_3          66                 0
  CLUS_4           7                27
D25V5, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           8                44
  CLUS_2          10                52
  CLUS_3          25                43
  CLUS_4          34                40
D25V6, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           4                 4
  CLUS_2          30                99
  CLUS_3          43                76
D25V7, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           2                92
  CLUS_2          31                47
  CLUS_3          44                53
D25V8, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1          36                 0
  CLUS_2           4               137
  CLUS_3          37                55
D25V9, multiclass
D25V10, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           0                14
  CLUS_2          26               119
  CLUS_3          51                58
D25V11, multiclass
D25V12, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           1                41
  CLUS_2          19                86
  CLUS_3          57                64

Clustering(26) Variable = 1q loss
D26V1, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0                 9
  CLUS_2           3                 7
  CLUS_3           0                 8
D26V2, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           3                 4
  CLUS_2           0                 6
  CLUS_3           0                10
  CLUS_4           0                 4
D26V3, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0                52
  CLUS_2           0                57
  CLUS_3           3                51
  CLUS_4           7                99
D26V4, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           1               121
  CLUS_2           0                42
  CLUS_3           9                57
  CLUS_4           0                34
D26V5, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0                52
  CLUS_2           0                62
  CLUS_3           4                64
  CLUS_4           6                68
D26V6, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           5               124
  CLUS_3           5               114
D26V7, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0                94
  CLUS_2           4                74
  CLUS_3           6                91
D26V8, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           5                31
  CLUS_2           0               141
  CLUS_3           5                87
D26V9, multiclass
D26V10, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0                14
  CLUS_2           5               140
  CLUS_3           5               104
D26V11, multiclass
D26V12, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0                42
  CLUS_2           2               103
  CLUS_3           8               113

Clustering(27) Variable = 2p loss
D27V1, multiclass
D27V2, multiclass
D27V3, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           2                50
  CLUS_2           0                57
  CLUS_3           4                50
  CLUS_4           0               106
D27V4, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           3               119
  CLUS_2           1                41
  CLUS_3           1                65
  CLUS_4           1                33
D27V5, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           2                50
  CLUS_2           3                59
  CLUS_3           0                68
  CLUS_4           1                73
D27V6, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           3               126
  CLUS_3           3               116
D27V7, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           5                89
  CLUS_2           1                77
  CLUS_3           0                97
D27V8, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           1                35
  CLUS_2           5               136
  CLUS_3           0                92
D27V9, multiclass
D27V10, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           0                14
  CLUS_2           5               140
  CLUS_3           1               108
D27V11, multiclass
D27V12, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           1                41
  CLUS_2           3               102
  CLUS_3           2               119

Clustering(28) Variable = 2q loss
D28V1, multiclass
[1] "Remove cluster labels:" "2Q LOSS CNV"           
clus
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D28V2, multiclass
[1] "Remove cluster labels:" "2Q LOSS CNV"           
clus
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D28V3, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           2                50
  CLUS_2           0                57
  CLUS_3           2                52
  CLUS_4           0               106
D28V4, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           2               120
  CLUS_2           0                42
  CLUS_3           1                65
  CLUS_4           1                33
D28V5, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           2                50
  CLUS_2           1                61
  CLUS_3           0                68
  CLUS_4           1                73
D28V6, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           2               127
  CLUS_3           2               117
D28V7, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           2                92
  CLUS_2           2                76
  CLUS_3           0                97
D28V8, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1                35
  CLUS_2           3               138
  CLUS_3           0                92
D28V9, multiclass
D28V10, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           0                14
  CLUS_2           3               142
  CLUS_3           1               108
D28V11, multiclass
D28V12, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           0                42
  CLUS_2           3               102
  CLUS_3           1               120

Clustering(29) Variable = 3p loss
D29V1, multiclass
[1] "Remove cluster labels:" "3P LOSS CNV"           
clus
      3P LOSS CNV 3P LOSS WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
D29V2, multiclass
[1] "Remove cluster labels:" "3P LOSS CNV"           
clus
      3P LOSS CNV 3P LOSS WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
D29V3, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           4                48
  CLUS_2           1                56
  CLUS_3           5                49
  CLUS_4           0               106
D29V4, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           7               115
  CLUS_2           2                40
  CLUS_3           0                66
  CLUS_4           1                33
D29V5, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           1                51
  CLUS_2           7                55
  CLUS_3           0                68
  CLUS_4           1                73
D29V6, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           8               121
  CLUS_3           1               118
D29V7, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           9                85
  CLUS_2           1                77
  CLUS_3           0                97
D29V8, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           0                36
  CLUS_2          10               131
  CLUS_3           0                92
D29V9, multiclass
D29V10, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           0                14
  CLUS_2           8               137
  CLUS_3           2               107
D29V11, multiclass
D29V12, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           3                39
  CLUS_2           6                99
  CLUS_3           1               120

Clustering(30) Variable = 3q loss
D30V1, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           1                 8
  CLUS_2           0                10
  CLUS_3           2                 6
D30V2, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           0                 7
  CLUS_2           1                 5
  CLUS_3           1                 9
  CLUS_4           1                 3
D30V3, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           8                44
  CLUS_2           0                57
  CLUS_3           5                49
  CLUS_4           0               106
D30V4, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1          10               112
  CLUS_2           1                41
  CLUS_3           0                66
  CLUS_4           2                32
D30V5, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           2                50
  CLUS_2           7                55
  CLUS_3           3                65
  CLUS_4           1                73
D30V6, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           0                 8
  CLUS_2          11               118
  CLUS_3           2               117
D30V7, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           9                85
  CLUS_2           2                76
  CLUS_3           2                95
D30V8, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           0                36
  CLUS_2          11               130
  CLUS_3           2                90
D30V9, multiclass
D30V10, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           1                13
  CLUS_2           8               137
  CLUS_3           4               105
D30V11, multiclass
D30V12, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           3                39
  CLUS_2           8                97
  CLUS_3           2               119

Clustering(31) Variable = 4p loss
D31V1, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           0                 9
  CLUS_2           2                 8
  CLUS_3           2                 6
D31V2, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           1                 6
  CLUS_2           1                 5
  CLUS_3           0                10
  CLUS_4           2                 2
D31V3, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           0                52
  CLUS_2           0                57
  CLUS_3           8                46
  CLUS_4          10                96
D31V4, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           3               119
  CLUS_2           0                42
  CLUS_3          15                51
  CLUS_4           0                34
D31V5, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           2                50
  CLUS_2           4                58
  CLUS_3           5                63
  CLUS_4           7                67
D31V6, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           1                 7
  CLUS_2           9               120
  CLUS_3           8               111
D31V7, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           0                94
  CLUS_2          10                68
  CLUS_3           8                89
D31V8, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1          10                26
  CLUS_2           2               139
  CLUS_3           6                86
D31V9, multiclass
D31V10, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           0                14
  CLUS_2          10               135
  CLUS_3           8               101
D31V11, multiclass
D31V12, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           0                42
  CLUS_2           8                97
  CLUS_3          10               111

Clustering(32) Variable = 4q loss
D32V1, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           1                 8
  CLUS_2           2                 8
  CLUS_3           2                 6
D32V2, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           1                 6
  CLUS_2           1                 5
  CLUS_3           1                 9
  CLUS_4           2                 2
D32V3, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           4                48
  CLUS_2           0                57
  CLUS_3          12                42
  CLUS_4          12                94
D32V4, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           9               113
  CLUS_2           0                42
  CLUS_3          18                48
  CLUS_4           1                33
D32V5, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           3                49
  CLUS_2           8                54
  CLUS_3           7                61
  CLUS_4           9                65
D32V6, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           1                 7
  CLUS_2          12               117
  CLUS_3          14               105
D32V7, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           2                92
  CLUS_2          16                62
  CLUS_3          10                87
D32V8, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1          12                24
  CLUS_2           8               133
  CLUS_3           8                84
D32V9, multiclass
D32V10, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           1                13
  CLUS_2          14               131
  CLUS_3          13                96
D32V11, multiclass
D32V12, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           1                41
  CLUS_2           9                96
  CLUS_3          18               103

Clustering(33) Variable = 5p loss
D33V1, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           2                 7
  CLUS_2           2                 8
  CLUS_3           2                 6
D33V2, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           0                 7
  CLUS_2           1                 5
  CLUS_3           2                 8
  CLUS_4           3                 1
D33V3, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           5                47
  CLUS_2           1                56
  CLUS_3           6                48
  CLUS_4           1               105
D33V4, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1          10               112
  CLUS_2           1                41
  CLUS_3           1                65
  CLUS_4           1                33
D33V5, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           2                50
  CLUS_2           5                57
  CLUS_3           2                66
  CLUS_4           4                70
D33V6, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           7               122
  CLUS_3           6               113
D33V7, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           5                89
  CLUS_2           3                75
  CLUS_3           5                92
D33V8, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           0                36
  CLUS_2           8               133
  CLUS_3           5                87
D33V9, multiclass
D33V10, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           0                14
  CLUS_2           6               139
  CLUS_3           7               102
D33V11, multiclass
D33V12, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           1                41
  CLUS_2           6                99
  CLUS_3           6               115

Clustering(34) Variable = 5q loss
D34V1, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           0                 9
  CLUS_2           2                 8
  CLUS_3           2                 6
D34V2, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           0                 7
  CLUS_2           1                 5
  CLUS_3           0                10
  CLUS_4           3                 1
D34V3, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           4                48
  CLUS_2           0                57
  CLUS_3           6                48
  CLUS_4           1               105
D34V4, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           9               113
  CLUS_2           1                41
  CLUS_3           1                65
  CLUS_4           0                34
D34V5, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           3                49
  CLUS_2           6                56
  CLUS_3           2                66
  CLUS_4           0                74
D34V6, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           6               123
  CLUS_3           5               114
D34V7, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           7                87
  CLUS_2           2                76
  CLUS_3           2                95
D34V8, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           0                36
  CLUS_2           9               132
  CLUS_3           2                90
D34V9, multiclass
D34V10, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           1                13
  CLUS_2           7               138
  CLUS_3           3               106
D34V11, multiclass
D34V12, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           3                39
  CLUS_2           5               100
  CLUS_3           3               118

Clustering(35) Variable = 6p loss
D35V1, multiclass
D35V2, multiclass
D35V3, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           2                50
  CLUS_2           4                53
  CLUS_3           3                51
  CLUS_4           1               105
D35V4, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           1               121
  CLUS_2           5                37
  CLUS_3           2                64
  CLUS_4           2                32
D35V5, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           4                48
  CLUS_2           3                59
  CLUS_3           0                68
  CLUS_4           2                72
D35V6, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           4               125
  CLUS_3           5               114
D35V7, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           6                88
  CLUS_2           1                77
  CLUS_3           3                94
D35V8, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           1                35
  CLUS_2           6               135
  CLUS_3           3                89
D35V9, multiclass
D35V10, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           2                12
  CLUS_2           6               139
  CLUS_3           2               107
D35V11, multiclass
D35V12, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           5                37
  CLUS_2           4               101
  CLUS_3           1               120

Clustering(36) Variable = 6q loss
D36V1, multiclass
[1] "Remove cluster labels:" "6Q LOSS CNV"           
clus
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-5390        TCGA-CS-5394 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270        TCGA-DB-5273 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276        TCGA-DB-5277 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5281        TCGA-DH-5140        TCGA-DH-5141 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144        TCGA-E1-5302 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-E1-5322 
"6Q LOSS WILD-TYPE" 
D36V2, multiclass
[1] "Remove cluster labels:" "6Q LOSS CNV"           
clus
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-5390        TCGA-CS-5394 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270        TCGA-DB-5273 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276        TCGA-DB-5277 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5281        TCGA-DH-5140        TCGA-DH-5141 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144        TCGA-E1-5302 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-E1-5322 
"6Q LOSS WILD-TYPE" 
D36V3, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           3                49
  CLUS_2           9                48
  CLUS_3          15                39
  CLUS_4           5               101
D36V4, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          19               103
  CLUS_2           8                34
  CLUS_3           2                64
  CLUS_4           3                31
D36V5, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           6                46
  CLUS_2          12                50
  CLUS_3           5                63
  CLUS_4           8                66
D36V6, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           1                 7
  CLUS_2          17               112
  CLUS_3          13               106
D36V7, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          14                80
  CLUS_2           7                71
  CLUS_3          11                86
D36V8, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           1                35
  CLUS_2          19               122
  CLUS_3          12                80
D36V9, multiclass
D36V10, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           2                12
  CLUS_2          20               125
  CLUS_3          10                99
D36V11, multiclass
D36V12, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           6                36
  CLUS_2          17                88
  CLUS_3           9               112

Clustering(37) Variable = 8p loss
D37V1, multiclass
[1] "Remove cluster labels:" "8P LOSS CNV"           
clus
      8P LOSS CNV 8P LOSS WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5141 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144        TCGA-E1-5302 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E1-5322 
"8P LOSS WILD-TYPE" 
D37V2, multiclass
[1] "Remove cluster labels:" "8P LOSS CNV"           
clus
      8P LOSS CNV 8P LOSS WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5141 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144        TCGA-E1-5302 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E1-5322 
"8P LOSS WILD-TYPE" 
D37V3, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           1                51
  CLUS_2           1                56
  CLUS_3           4                50
  CLUS_4           0               106
D37V4, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           2               120
  CLUS_2           3                39
  CLUS_3           0                66
  CLUS_4           1                33
D37V5, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           1                51
  CLUS_2           3                59
  CLUS_3           0                68
  CLUS_4           1                73
D37V6, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           4               125
  CLUS_3           1               118
D37V7, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           4                90
  CLUS_2           1                77
  CLUS_3           1                96
D37V8, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           0                36
  CLUS_2           5               136
  CLUS_3           1                91
D37V9, multiclass
D37V10, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           1                13
  CLUS_2           4               141
  CLUS_3           1               108
D37V11, multiclass
D37V12, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           2                40
  CLUS_2           4               101
  CLUS_3           0               121

Clustering(38) Variable = 8q loss
D38V1, multiclass
[1] "Remove cluster labels:" "8Q LOSS CNV"           
clus
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D38V2, multiclass
[1] "Remove cluster labels:" "8Q LOSS CNV"           
clus
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D38V3, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           1                51
  CLUS_2           1                56
  CLUS_3           2                52
  CLUS_4           0               106
D38V4, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           0               122
  CLUS_2           3                39
  CLUS_3           0                66
  CLUS_4           1                33
D38V5, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           1                51
  CLUS_2           1                61
  CLUS_3           0                68
  CLUS_4           1                73
D38V6, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           2               127
  CLUS_3           1               118
D38V7, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           3                91
  CLUS_2           0                78
  CLUS_3           1                96
D38V8, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           0                36
  CLUS_2           3               138
  CLUS_3           1                91
D38V9, multiclass
D38V10, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           1                13
  CLUS_2           3               142
  CLUS_3           0               109
D38V11, multiclass
D38V12, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           2                40
  CLUS_2           2               103
  CLUS_3           0               121

Clustering(39) Variable = 9p loss
D39V1, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           1                 8
  CLUS_2           0                10
  CLUS_3           3                 5
D39V2, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           0                 7
  CLUS_2           1                 5
  CLUS_3           2                 8
  CLUS_4           1                 3
D39V3, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           5                47
  CLUS_2          18                39
  CLUS_3          18                36
  CLUS_4           8                98
D39V4, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          29                93
  CLUS_2          10                32
  CLUS_3           6                60
  CLUS_4           3                31
D39V5, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           6                46
  CLUS_2          18                44
  CLUS_3          12                56
  CLUS_4           9                65
D39V6, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           2                 6
  CLUS_2          29               100
  CLUS_3          14               105
D39V7, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          18                76
  CLUS_2          15                63
  CLUS_3          16                81
D39V8, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           5                31
  CLUS_2          30               111
  CLUS_3          14                78
D39V9, multiclass
D39V10, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           5                 9
  CLUS_2          26               119
  CLUS_3          18                91
D39V11, multiclass
D39V12, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          10                32
  CLUS_2          20                85
  CLUS_3          19               102

Clustering(40) Variable = 9q loss
D40V1, multiclass
D40V2, multiclass
D40V3, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           1                51
  CLUS_2           0                57
  CLUS_3           4                50
  CLUS_4           2               104
D40V4, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           1               121
  CLUS_2           0                42
  CLUS_3           5                61
  CLUS_4           1                33
D40V5, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           2                50
  CLUS_2           1                61
  CLUS_3           2                66
  CLUS_4           2                72
D40V6, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           1                 7
  CLUS_2           3               126
  CLUS_3           3               116
D40V7, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           1                93
  CLUS_2           3                75
  CLUS_3           3                94
D40V8, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           4                32
  CLUS_2           1               140
  CLUS_3           2                90
D40V9, multiclass
D40V10, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           0                14
  CLUS_2           5               140
  CLUS_3           2               107
D40V11, multiclass
D40V12, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           0                42
  CLUS_2           2               103
  CLUS_3           5               116

Clustering(41) Variable = 10p loss
D41V1, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            0                  9
  CLUS_2            1                  9
  CLUS_3            2                  6
D41V2, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            0                  7
  CLUS_2            1                  5
  CLUS_3            1                  9
  CLUS_4            1                  3
D41V3, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            1                 51
  CLUS_2           28                 29
  CLUS_3            5                 49
  CLUS_4            2                104
D41V4, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            1                121
  CLUS_2           31                 11
  CLUS_3            3                 63
  CLUS_4            0                 34
D41V5, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            4                 48
  CLUS_2           21                 41
  CLUS_3            3                 65
  CLUS_4            3                 71
D41V6, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            1                  7
  CLUS_2           25                104
  CLUS_3            5                114
D41V7, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1           31                 63
  CLUS_2            1                 77
  CLUS_3            4                 93
D41V8, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            1                 35
  CLUS_2           31                110
  CLUS_3            4                 88
D41V9, multiclass
D41V10, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            8                  6
  CLUS_2           24                121
  CLUS_3            4                105
D41V11, multiclass
D41V12, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1           23                 19
  CLUS_2            9                 96
  CLUS_3            4                117

Clustering(42) Variable = 10q loss
D42V1, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            0                  9
  CLUS_2            1                  9
  CLUS_3            2                  6
D42V2, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            0                  7
  CLUS_2            1                  5
  CLUS_3            1                  9
  CLUS_4            1                  3
D42V3, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            2                 50
  CLUS_2           28                 29
  CLUS_3            6                 48
  CLUS_4            2                104
D42V4, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            3                119
  CLUS_2           31                 11
  CLUS_3            3                 63
  CLUS_4            0                 34
D42V5, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            5                 47
  CLUS_2           21                 41
  CLUS_3            4                 64
  CLUS_4            3                 71
D42V6, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            1                  7
  CLUS_2           26                103
  CLUS_3            6                113
D42V7, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           32                 62
  CLUS_2            1                 77
  CLUS_3            5                 92
D42V8, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            1                 35
  CLUS_2           32                109
  CLUS_3            5                 87
D42V9, multiclass
D42V10, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            9                  5
  CLUS_2           24                121
  CLUS_3            5                104
D42V11, multiclass
D42V12, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           24                 18
  CLUS_2            9                 96
  CLUS_3            5                116

Clustering(43) Variable = 11p loss
D43V1, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            2                  7
  CLUS_2            1                  9
  CLUS_3            1                  7
D43V2, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            0                  7
  CLUS_2            0                  6
  CLUS_3            2                  8
  CLUS_4            2                  2
D43V3, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1           12                 40
  CLUS_2            2                 55
  CLUS_3           11                 43
  CLUS_4            0                106
D43V4, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1           21                101
  CLUS_2            2                 40
  CLUS_3            0                 66
  CLUS_4            2                 32
D43V5, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            7                 45
  CLUS_2           11                 51
  CLUS_3            3                 65
  CLUS_4            4                 70
D43V6, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            1                  7
  CLUS_2           14                115
  CLUS_3           10                109
D43V7, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1           16                 78
  CLUS_2            3                 75
  CLUS_3            6                 91
D43V8, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            0                 36
  CLUS_2           20                121
  CLUS_3            5                 87
D43V9, multiclass
D43V10, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            1                 13
  CLUS_2           16                129
  CLUS_3            8                101
D43V11, multiclass
D43V12, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            6                 36
  CLUS_2           12                 93
  CLUS_3            7                114

Clustering(44) Variable = 11q loss
D44V1, multiclass
[1] "Remove cluster labels:" "11Q LOSS CNV"          
clus
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-E1-5302         TCGA-E1-5303         TCGA-E1-5311 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
D44V2, multiclass
[1] "Remove cluster labels:" "11Q LOSS CNV"          
clus
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-E1-5302         TCGA-E1-5303         TCGA-E1-5311 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
D44V3, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            2                 50
  CLUS_2            1                 56
  CLUS_3            4                 50
  CLUS_4            0                106
D44V4, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            4                118
  CLUS_2            2                 40
  CLUS_3            0                 66
  CLUS_4            1                 33
D44V5, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            1                 51
  CLUS_2            5                 57
  CLUS_3            0                 68
  CLUS_4            1                 73
D44V6, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            4                125
  CLUS_3            3                116
D44V7, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            6                 88
  CLUS_2            0                 78
  CLUS_3            1                 96
D44V8, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            0                 36
  CLUS_2            6                135
  CLUS_3            1                 91
D44V9, multiclass
D44V10, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            5                140
  CLUS_3            2                107
D44V11, multiclass
D44V12, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            1                 41
  CLUS_2            4                101
  CLUS_3            2                119

Clustering(45) Variable = 12p loss
D45V1, multiclass
D45V2, multiclass
D45V3, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            0                 52
  CLUS_2            0                 57
  CLUS_3            2                 52
  CLUS_4            2                104
D45V4, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            2                120
  CLUS_2            0                 42
  CLUS_3            2                 64
  CLUS_4            0                 34
D45V5, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            2                 50
  CLUS_2            1                 61
  CLUS_3            1                 67
  CLUS_4            0                 74
D45V6, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            2                127
  CLUS_3            2                117
D45V7, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            2                 92
  CLUS_2            0                 78
  CLUS_3            2                 95
D45V8, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            0                 36
  CLUS_2            2                139
  CLUS_3            2                 90
D45V9, multiclass
D45V10, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            1                 13
  CLUS_2            2                143
  CLUS_3            1                108
D45V11, multiclass
D45V12, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            1                 41
  CLUS_2            1                104
  CLUS_3            2                119

Clustering(46) Variable = 12q loss
D46V1, multiclass
[1] "Remove cluster labels:" "12Q LOSS CNV"          
clus
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
D46V2, multiclass
[1] "Remove cluster labels:" "12Q LOSS CNV"          
clus
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
D46V3, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            6                 46
  CLUS_2            0                 57
  CLUS_3            3                 51
  CLUS_4            2                104
D46V4, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            9                113
  CLUS_2            0                 42
  CLUS_3            2                 64
  CLUS_4            0                 34
D46V5, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            2                 50
  CLUS_2            3                 59
  CLUS_3            5                 63
  CLUS_4            1                 73
D46V6, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            1                  7
  CLUS_2            6                123
  CLUS_3            4                115
D46V7, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            7                 87
  CLUS_2            1                 77
  CLUS_3            3                 94
D46V8, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            0                 36
  CLUS_2            8                133
  CLUS_3            3                 89
D46V9, multiclass
D46V10, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            2                 12
  CLUS_2            6                139
  CLUS_3            3                106
D46V11, multiclass
D46V12, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            3                 39
  CLUS_2            4                101
  CLUS_3            4                117

Clustering(47) Variable = 13q loss
D47V1, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            2                  7
  CLUS_2            2                  8
  CLUS_3            1                  7
D47V2, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            0                  7
  CLUS_2            0                  6
  CLUS_3            2                  8
  CLUS_4            3                  1
D47V3, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            3                 49
  CLUS_2            1                 56
  CLUS_3           27                 27
  CLUS_4            0                106
D47V4, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           18                104
  CLUS_2            6                 36
  CLUS_3            7                 59
  CLUS_4            0                 34
D47V5, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            3                 49
  CLUS_2           13                 49
  CLUS_3            7                 61
  CLUS_4            8                 66
D47V6, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            1                  7
  CLUS_2           15                114
  CLUS_3           15                104
D47V7, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           12                 82
  CLUS_2           11                 67
  CLUS_3            8                 89
D47V8, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            5                 31
  CLUS_2           20                121
  CLUS_3            6                 86
D47V9, multiclass
D47V10, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            2                 12
  CLUS_2           19                126
  CLUS_3           10                 99
D47V11, multiclass
D47V12, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            2                 40
  CLUS_2           16                 89
  CLUS_3           13                108

Clustering(48) Variable = 14q loss
D48V1, multiclass
[1] "Remove cluster labels:" "14Q LOSS CNV"          
clus
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                 2                 25 
        TCGA-CS-4943         TCGA-CS-4944         TCGA-CS-5390 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CS-5394         TCGA-CS-5395         TCGA-CS-5396 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DH-5141         TCGA-DH-5142         TCGA-DH-5143 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DH-5144         TCGA-E1-5302         TCGA-E1-5303 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-E1-5304         TCGA-E1-5311         TCGA-E1-5318 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-E1-5322 
"14Q LOSS WILD-TYPE" 
D48V2, multiclass
[1] "Remove cluster labels:" "14Q LOSS CNV"          
clus
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                 2                 25 
        TCGA-CS-4943         TCGA-CS-4944         TCGA-CS-5390 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CS-5394         TCGA-CS-5395         TCGA-CS-5396 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DH-5141         TCGA-DH-5142         TCGA-DH-5143 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DH-5144         TCGA-E1-5302         TCGA-E1-5303 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-E1-5304         TCGA-E1-5311         TCGA-E1-5318 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-E1-5322 
"14Q LOSS WILD-TYPE" 
D48V3, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            3                 49
  CLUS_2            8                 49
  CLUS_3           11                 43
  CLUS_4            6                100
D48V4, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           10                112
  CLUS_2           12                 30
  CLUS_3            6                 60
  CLUS_4            0                 34
D48V5, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            3                 49
  CLUS_2           12                 50
  CLUS_3            6                 62
  CLUS_4            5                 69
D48V6, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            0                  8
  CLUS_2           17                112
  CLUS_3            9                110
D48V7, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           17                 77
  CLUS_2            4                 74
  CLUS_3            7                 90
D48V8, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            2                 34
  CLUS_2           20                121
  CLUS_3            6                 86
D48V9, multiclass
D48V10, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            2                 12
  CLUS_2           22                123
  CLUS_3            4                105
D48V11, multiclass
D48V12, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            6                 36
  CLUS_2           14                 91
  CLUS_3            8                113

Clustering(49) Variable = 15q loss
D49V1, multiclass
[1] "Remove cluster labels:" "15Q LOSS CNV"          
clus
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-E1-5302         TCGA-E1-5303         TCGA-E1-5304 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
D49V2, multiclass
[1] "Remove cluster labels:" "15Q LOSS CNV"          
clus
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-E1-5302         TCGA-E1-5303         TCGA-E1-5304 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
D49V3, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            1                 51
  CLUS_2            2                 55
  CLUS_3            5                 49
  CLUS_4            8                 98
D49V4, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            3                119
  CLUS_2            2                 40
  CLUS_3           11                 55
  CLUS_4            0                 34
D49V5, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            2                 50
  CLUS_2            6                 56
  CLUS_3            5                 63
  CLUS_4            3                 71
D49V6, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            1                  7
  CLUS_2           12                117
  CLUS_3            3                116
D49V7, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            5                 89
  CLUS_2            6                 72
  CLUS_3            5                 92
D49V8, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            7                 29
  CLUS_2            5                136
  CLUS_3            4                 88
D49V9, multiclass
D49V10, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            1                 13
  CLUS_2            9                136
  CLUS_3            6                103
D49V11, multiclass
D49V12, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            2                 40
  CLUS_2            8                 97
  CLUS_3            6                115

Clustering(50) Variable = 16p loss
D50V1, multiclass
[1] "Remove cluster labels:" "16P LOSS CNV"          
clus
      16P LOSS CNV 16P LOSS WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DH-5140 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DH-5141         TCGA-DH-5142         TCGA-DH-5143 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DH-5144         TCGA-E1-5302         TCGA-E1-5303 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-E1-5304         TCGA-E1-5311         TCGA-E1-5318 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-E1-5322 
"16P LOSS WILD-TYPE" 
D50V2, multiclass
[1] "Remove cluster labels:" "16P LOSS CNV"          
clus
      16P LOSS CNV 16P LOSS WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DH-5140 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DH-5141         TCGA-DH-5142         TCGA-DH-5143 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DH-5144         TCGA-E1-5302         TCGA-E1-5303 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-E1-5304         TCGA-E1-5311         TCGA-E1-5318 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-E1-5322 
"16P LOSS WILD-TYPE" 
D50V3, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            1                 51
  CLUS_2            0                 57
  CLUS_3            2                 52
  CLUS_4            0                106
D50V4, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            3                119
  CLUS_2            0                 42
  CLUS_3            0                 66
  CLUS_4            0                 34
D50V5, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            0                 52
  CLUS_2            2                 60
  CLUS_3            1                 67
  CLUS_4            0                 74
D50V6, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            3                126
  CLUS_3            0                119
D50V7, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            1                 93
  CLUS_2            1                 77
  CLUS_3            1                 96
D50V8, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            0                 36
  CLUS_2            2                139
  CLUS_3            1                 91
D50V9, multiclass
D50V10, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            0                145
  CLUS_3            3                106
D50V11, multiclass
D50V12, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            0                 42
  CLUS_2            3                102
  CLUS_3            0                121

Clustering(51) Variable = 16q loss
D51V1, multiclass
[1] "Remove cluster labels:" "16Q LOSS CNV"          
clus
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D51V2, multiclass
[1] "Remove cluster labels:" "16Q LOSS CNV"          
clus
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D51V3, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            3                 49
  CLUS_2            2                 55
  CLUS_3            2                 52
  CLUS_4            0                106
D51V4, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            3                119
  CLUS_2            4                 38
  CLUS_3            0                 66
  CLUS_4            0                 34
D51V5, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            0                 52
  CLUS_2            3                 59
  CLUS_3            3                 65
  CLUS_4            0                 74
D51V6, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            5                124
  CLUS_3            1                118
D51V7, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            5                 89
  CLUS_2            1                 77
  CLUS_3            1                 96
D51V8, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            0                 36
  CLUS_2            6                135
  CLUS_3            1                 91
D51V9, multiclass
D51V10, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            1                 13
  CLUS_2            5                140
  CLUS_3            1                108
D51V11, multiclass
D51V12, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            2                 40
  CLUS_2            4                101
  CLUS_3            1                120

Clustering(52) Variable = 17p loss
D52V1, multiclass
D52V2, multiclass
D52V3, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            1                 51
  CLUS_2            2                 55
  CLUS_3            1                 53
  CLUS_4            0                106
D52V4, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            1                121
  CLUS_2            2                 40
  CLUS_3            0                 66
  CLUS_4            1                 33
D52V5, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            1                 51
  CLUS_2            2                 60
  CLUS_3            0                 68
  CLUS_4            0                 74
D52V6, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            2                127
  CLUS_3            1                118
D52V7, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            4                 90
  CLUS_2            0                 78
  CLUS_3            0                 97
D52V8, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            0                 36
  CLUS_2            4                137
  CLUS_3            0                 92
D52V9, multiclass
D52V10, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            4                141
  CLUS_3            0                109
D52V11, multiclass
D52V12, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            2                 40
  CLUS_2            1                104
  CLUS_3            1                120

Clustering(53) Variable = 18p loss
D53V1, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            1                  8
  CLUS_2            3                  7
  CLUS_3            0                  8
D53V2, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            1                  6
  CLUS_2            0                  6
  CLUS_3            1                  9
  CLUS_4            2                  2
D53V3, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            0                 52
  CLUS_2            4                 53
  CLUS_3            8                 46
  CLUS_4            9                 97
D53V4, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            6                116
  CLUS_2            4                 38
  CLUS_3           11                 55
  CLUS_4            0                 34
D53V5, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            4                 48
  CLUS_2            7                 55
  CLUS_3            6                 62
  CLUS_4            4                 70
D53V6, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            0                  8
  CLUS_2           15                114
  CLUS_3            6                113
D53V7, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            8                 86
  CLUS_2            7                 71
  CLUS_3            6                 91
D53V8, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            5                 31
  CLUS_2           10                131
  CLUS_3            6                 86
D53V9, multiclass
D53V10, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            1                 13
  CLUS_2           15                130
  CLUS_3            5                104
D53V11, multiclass
D53V12, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            2                 40
  CLUS_2           13                 92
  CLUS_3            6                115

Clustering(54) Variable = 18q loss
D54V1, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            0                  9
  CLUS_2            3                  7
  CLUS_3            0                  8
D54V2, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            1                  6
  CLUS_2            0                  6
  CLUS_3            0                 10
  CLUS_4            2                  2
D54V3, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            0                 52
  CLUS_2            3                 54
  CLUS_3            8                 46
  CLUS_4            9                 97
D54V4, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            4                118
  CLUS_2            4                 38
  CLUS_3           12                 54
  CLUS_4            0                 34
D54V5, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            2                 50
  CLUS_2            8                 54
  CLUS_3            6                 62
  CLUS_4            4                 70
D54V6, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            0                  8
  CLUS_2           14                115
  CLUS_3            6                113
D54V7, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            6                 88
  CLUS_2            8                 70
  CLUS_3            6                 91
D54V8, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            6                 30
  CLUS_2            8                133
  CLUS_3            6                 86
D54V9, multiclass
D54V10, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            1                 13
  CLUS_2           13                132
  CLUS_3            6                103
D54V11, multiclass
D54V12, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            2                 40
  CLUS_2           12                 93
  CLUS_3            6                115

Clustering(55) Variable = 19p loss
D55V1, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            0                  9
  CLUS_2            2                  8
  CLUS_3            1                  7
D55V2, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            2                  5
  CLUS_2            0                  6
  CLUS_3            0                 10
  CLUS_4            1                  3
D55V3, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                 51
  CLUS_2            0                 57
  CLUS_3            2                 52
  CLUS_4            4                102
D55V4, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                121
  CLUS_2            1                 41
  CLUS_3            4                 62
  CLUS_4            1                 33
D55V5, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                 51
  CLUS_2            2                 60
  CLUS_3            2                 66
  CLUS_4            2                 72
D55V6, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                  7
  CLUS_2            5                124
  CLUS_3            1                118
D55V7, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                 93
  CLUS_2            4                 74
  CLUS_3            2                 95
D55V8, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            3                 33
  CLUS_2            2                139
  CLUS_3            2                 90
D55V9, multiclass
D55V10, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                 13
  CLUS_2            4                141
  CLUS_3            2                107
D55V11, multiclass
D55V12, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                 41
  CLUS_2            4                101
  CLUS_3            2                119

Clustering(56) Variable = 19q loss
D56V1, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            2                  7
  CLUS_2            6                  4
  CLUS_3            3                  5
D56V2, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            6                  1
  CLUS_2            2                  4
  CLUS_3            2                  8
  CLUS_4            1                  3
D56V3, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            1                 51
  CLUS_2            0                 57
  CLUS_3           20                 34
  CLUS_4           64                 42
D56V4, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            7                115
  CLUS_2            2                 40
  CLUS_3           64                  2
  CLUS_4            9                 25
D56V5, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            8                 44
  CLUS_2           16                 46
  CLUS_3           24                 44
  CLUS_4           37                 37
D56V6, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            4                  4
  CLUS_2           35                 94
  CLUS_3           46                 73
D56V7, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            5                 89
  CLUS_2           33                 45
  CLUS_3           47                 50
D56V8, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1           35                  1
  CLUS_2            9                132
  CLUS_3           41                 51
D56V9, multiclass
D56V10, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            1                 13
  CLUS_2           30                115
  CLUS_3           54                 55
D56V11, multiclass
D56V12, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            3                 39
  CLUS_2           23                 82
  CLUS_3           59                 62

Clustering(57) Variable = 20p loss
D57V1, multiclass
[1] "Remove cluster labels:" "20P LOSS CNV"          
clus
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
D57V2, multiclass
[1] "Remove cluster labels:" "20P LOSS CNV"          
clus
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
D57V3, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            1                 51
  CLUS_2            1                 56
  CLUS_3            1                 53
  CLUS_4            0                106
D57V4, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            3                119
  CLUS_2            0                 42
  CLUS_3            0                 66
  CLUS_4            0                 34
D57V5, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            1                 51
  CLUS_2            1                 61
  CLUS_3            0                 68
  CLUS_4            1                 73
D57V6, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            2                127
  CLUS_3            1                118
D57V7, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            1                 93
  CLUS_2            1                 77
  CLUS_3            1                 96
D57V8, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            0                 36
  CLUS_2            2                139
  CLUS_3            1                 91
D57V9, multiclass
D57V10, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            1                144
  CLUS_3            2                107
D57V11, multiclass
D57V12, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            0                 42
  CLUS_2            2                103
  CLUS_3            1                120

Clustering(58) Variable = 21q loss
D58V1, multiclass
[1] "Remove cluster labels:" "21Q LOSS CNV"          
clus
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-E1-5322 
"21Q LOSS WILD-TYPE" 
D58V2, multiclass
[1] "Remove cluster labels:" "21Q LOSS CNV"          
clus
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-E1-5322 
"21Q LOSS WILD-TYPE" 
D58V3, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            3                 49
  CLUS_2            1                 56
  CLUS_3            5                 49
  CLUS_4            2                104
D58V4, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            7                115
  CLUS_2            2                 40
  CLUS_3            1                 65
  CLUS_4            1                 33
D58V5, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            2                 50
  CLUS_2            4                 58
  CLUS_3            4                 64
  CLUS_4            1                 73
D58V6, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            7                122
  CLUS_3            4                115
D58V7, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            6                 88
  CLUS_2            2                 76
  CLUS_3            3                 94
D58V8, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            0                 36
  CLUS_2            9                132
  CLUS_3            2                 90
D58V9, multiclass
D58V10, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            1                 13
  CLUS_2           10                135
  CLUS_3            0                109
D58V11, multiclass
D58V12, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            2                 40
  CLUS_2            6                 99
  CLUS_3            3                118

Clustering(59) Variable = 22q loss
D59V1, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            1                  8
  CLUS_2            1                  9
  CLUS_3            1                  7
D59V2, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            0                  7
  CLUS_2            0                  6
  CLUS_3            1                  9
  CLUS_4            2                  2
D59V3, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            3                 49
  CLUS_2            8                 49
  CLUS_3            9                 45
  CLUS_4            0                106
D59V4, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            7                115
  CLUS_2           11                 31
  CLUS_3            0                 66
  CLUS_4            2                 32
D59V5, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            2                 50
  CLUS_2           14                 48
  CLUS_3            2                 66
  CLUS_4            2                 72
D59V6, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            0                  8
  CLUS_2           15                114
  CLUS_3            5                114
D59V7, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           15                 79
  CLUS_2            3                 75
  CLUS_3            2                 95
D59V8, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            0                 36
  CLUS_2           18                123
  CLUS_3            2                 90
D59V9, multiclass
D59V10, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            1                 13
  CLUS_2           14                131
  CLUS_3            5                104
D59V11, multiclass
D59V12, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            6                 36
  CLUS_2           11                 94
  CLUS_3            3                118

Clustering(60) Variable = Xq loss
D60V1, multiclass
D60V2, multiclass
D60V3, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           2                50
  CLUS_2           1                56
  CLUS_3           3                51
  CLUS_4           0               106
D60V4, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           3               119
  CLUS_2           2                40
  CLUS_3           0                66
  CLUS_4           1                33
D60V5, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           1                51
  CLUS_2           3                59
  CLUS_3           1                67
  CLUS_4           1                73
D60V6, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           5               124
  CLUS_3           1               118
D60V7, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           4                90
  CLUS_2           1                77
  CLUS_3           1                96
D60V8, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           0                36
  CLUS_2           5               136
  CLUS_3           1                91
D60V9, multiclass
D60V10, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           3                11
  CLUS_2           2               143
  CLUS_3           1               108
D60V11, multiclass
D60V12, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           3                39
  CLUS_2           2               103
  CLUS_3           1               120
                           V1                            V2 
                  "MRNA_CNMF"          "MRNA_CHIERARCHICAL" 
                           V3                            V4 
                    "CN_CNMF"            "METHLYATION_CNMF" 
                           V5                            V6 
                  "RPPA_CNMF"          "RPPA_CHIERARCHICAL" 
                           V7                            V8 
               "MRNASEQ_CNMF"       "MRNASEQ_CHIERARCHICAL" 
                           V9                           V10 
                "MIRSEQ_CNMF"        "MIRSEQ_CHIERARCHICAL" 
                          V11                           V12 
         "MIRSEQ_MATURE_CNMF" "MIRSEQ_MATURE_CHIERARCHICAL" 
> q(save="no")
