
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/3142714/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/LGG-TP/3144354/1.GDAC_mergedClustering.Finished/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=222, in cluster file=220, common to both=220
[1] "Reduce the number of clustering variables from 80 to 51."
[1]  51 220
[1] "1p gain"
[1] 3
      1P GAIN CNV 1P GAIN WILD-TYPE 
                6               214 
      1P GAIN CNV 1P GAIN WILD-TYPE 
                6               214 
[1] "1q gain"
[1] 3
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
                8               212 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
                8               212 
[1] "6p gain"
[1] 3
      6P GAIN CNV 6P GAIN WILD-TYPE 
                4               216 
      6P GAIN CNV 6P GAIN WILD-TYPE 
                4               216 
[1] "7p gain"
[1] 3
      7P GAIN CNV 7P GAIN WILD-TYPE 
               37               183 
      7P GAIN CNV 7P GAIN WILD-TYPE 
               37               183 
[1] "7q gain"
[1] 3
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               51               169 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               51               169 
[1] "8p gain"
[1] 3
      8P GAIN CNV 8P GAIN WILD-TYPE 
               14               206 
      8P GAIN CNV 8P GAIN WILD-TYPE 
               14               206 
[1] "8q gain"
[1] 3
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               17               203 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               17               203 
[1] "9p gain"
[1] 3
      9P GAIN CNV 9P GAIN WILD-TYPE 
                4               216 
      9P GAIN CNV 9P GAIN WILD-TYPE 
                4               216 
[1] "9q gain"
[1] 3
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                6               214 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                6               214 
[1] "10p gain"
[1] 3
      10P GAIN CNV 10P GAIN WILD-TYPE 
                21                199 
      10P GAIN CNV 10P GAIN WILD-TYPE 
                21                199 
[1] "11p gain"
[1] 3
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 9                211 
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 9                211 
[1] "11q gain"
[1] 3
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                14                206 
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                14                206 
[1] "12p gain"
[1] 3
      12P GAIN CNV 12P GAIN WILD-TYPE 
                11                209 
      12P GAIN CNV 12P GAIN WILD-TYPE 
                11                209 
[1] "12q gain"
[1] 3
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 5                215 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 5                215 
[1] "18p gain"
[1] 3
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 4                216 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 4                216 
[1] "19p gain"
[1] 3
      19P GAIN CNV 19P GAIN WILD-TYPE 
                11                209 
      19P GAIN CNV 19P GAIN WILD-TYPE 
                11                209 
[1] "19q gain"
[1] 3
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 9                211 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 9                211 
[1] "20p gain"
[1] 3
      20P GAIN CNV 20P GAIN WILD-TYPE 
                17                203 
      20P GAIN CNV 20P GAIN WILD-TYPE 
                17                203 
[1] "20q gain"
[1] 3
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                16                204 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                16                204 
[1] "21q gain"
[1] 3
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 3                217 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 3                217 
[1] "1p loss"
[1] 3
      1P LOSS CNV 1P LOSS WILD-TYPE 
               67               153 
      1P LOSS CNV 1P LOSS WILD-TYPE 
               67               153 
[1] "1q loss"
[1] 3
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                9               211 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                9               211 
[1] "2p loss"
[1] 3
      2P LOSS CNV 2P LOSS WILD-TYPE 
                4               216 
      2P LOSS CNV 2P LOSS WILD-TYPE 
                4               216 
[1] "2q loss"
[1] 3
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                3               217 
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                3               217 
[1] "3p loss"
[1] 3
      3P LOSS CNV 3P LOSS WILD-TYPE 
                4               216 
      3P LOSS CNV 3P LOSS WILD-TYPE 
                4               216 
[1] "3q loss"
[1] 3
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                9               211 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                9               211 
[1] "4p loss"
[1] 3
      4P LOSS CNV 4P LOSS WILD-TYPE 
               15               205 
      4P LOSS CNV 4P LOSS WILD-TYPE 
               15               205 
[1] "4q loss"
[1] 3
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               24               196 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               24               196 
[1] "5p loss"
[1] 3
      5P LOSS CNV 5P LOSS WILD-TYPE 
               11               209 
      5P LOSS CNV 5P LOSS WILD-TYPE 
               11               209 
[1] "5q loss"
[1] 3
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
                9               211 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
                9               211 
[1] "6p loss"
[1] 3
      6P LOSS CNV 6P LOSS WILD-TYPE 
                7               213 
      6P LOSS CNV 6P LOSS WILD-TYPE 
                7               213 
[1] "6q loss"
[1] 3
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               21               199 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               21               199 
[1] "8p loss"
[1] 3
      8P LOSS CNV 8P LOSS WILD-TYPE 
                3               217 
      8P LOSS CNV 8P LOSS WILD-TYPE 
                3               217 
[1] "9p loss"
[1] 3
      9P LOSS CNV 9P LOSS WILD-TYPE 
               38               182 
      9P LOSS CNV 9P LOSS WILD-TYPE 
               38               182 
[1] "9q loss"
[1] 3
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
                6               214 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
                6               214 
[1] "10p loss"
[1] 3
      10P LOSS CNV 10P LOSS WILD-TYPE 
                31                189 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                31                189 
[1] "10q loss"
[1] 3
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                32                188 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                32                188 
[1] "11p loss"
[1] 3
      11P LOSS CNV 11P LOSS WILD-TYPE 
                20                200 
      11P LOSS CNV 11P LOSS WILD-TYPE 
                20                200 
[1] "11q loss"
[1] 3
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 4                216 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 4                216 
[1] "12q loss"
[1] 3
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 8                212 
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 8                212 
[1] "13q loss"
[1] 3
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                28                192 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                28                192 
[1] "14q loss"
[1] 3
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                24                196 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                24                196 
[1] "15q loss"
[1] 3
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                12                208 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                12                208 
[1] "16q loss"
[1] 3
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 6                214 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 6                214 
[1] "18p loss"
[1] 3
      18P LOSS CNV 18P LOSS WILD-TYPE 
                15                205 
      18P LOSS CNV 18P LOSS WILD-TYPE 
                15                205 
[1] "18q loss"
[1] 3
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                16                204 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                16                204 
[1] "19p loss"
[1] 3
      19P LOSS CNV 19P LOSS WILD-TYPE 
                10                210 
      19P LOSS CNV 19P LOSS WILD-TYPE 
                10                210 
[1] "19q loss"
[1] 3
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                76                144 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                76                144 
[1] "21q loss"
[1] 3
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 8                212 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 8                212 
[1] "22q loss"
[1] 3
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                15                205 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                15                205 
[1] "Xq loss"
[1] 3
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                6               214 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                6               214 
[1] "data2feature, selection="
[1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
[4] "METHLYATION_CNMF"      "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL"
[7] "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 8 rows and 220 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
[4] "METHLYATION_CNMF"      "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL"
[7] "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 220 columns, 0 survival variables, and 8 non-survival variables.
MRNA_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=5, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_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           2                92
  CLUS_2           4                46
  CLUS_3           0                76
D1V4, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           3                97
  CLUS_2           3                31
  CLUS_3           0                58
  CLUS_4           0                23
D1V5, multiclass
D1V6, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           0                32
  CLUS_2           6               111
  CLUS_3           0                69
D1V7, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           3                55
  CLUS_2           0                32
  CLUS_3           1                81
  CLUS_4           2                45
D1V8, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           1                 7
  CLUS_2           1                94
  CLUS_3           4               112

Clustering(2) Variable = 1q gain
D2V1, multiclass
D2V2, multiclass
D2V3, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           2                92
  CLUS_2           6                44
  CLUS_3           0                76
D2V4, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           5                95
  CLUS_2           3                31
  CLUS_3           0                58
  CLUS_4           0                23
D2V5, multiclass
D2V6, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           0                32
  CLUS_2           6               111
  CLUS_3           2                67
D2V7, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           3                55
  CLUS_2           1                31
  CLUS_3           3                79
  CLUS_4           1                46
D2V8, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           1                 7
  CLUS_2           3                92
  CLUS_3           4               112

Clustering(3) Variable = 6p gain
D3V1, 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" 
D3V2, 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" 
D3V3, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           2                92
  CLUS_2           2                48
  CLUS_3           0                76
D3V4, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           4                96
  CLUS_2           0                34
  CLUS_3           0                58
  CLUS_4           0                23
D3V5, multiclass
D3V6, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           0                32
  CLUS_2           4               113
  CLUS_3           0                69
D3V7, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           2                56
  CLUS_2           0                32
  CLUS_3           0                82
  CLUS_4           2                45
D3V8, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           1                94
  CLUS_3           3               113

Clustering(4) Variable = 7p gain
D4V1, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           1                 8
  CLUS_2           0                10
  CLUS_3           2                 6
D4V2, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           1                 8
  CLUS_2           2                 5
  CLUS_3           0                11
D4V3, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           5                89
  CLUS_2          30                20
  CLUS_3           2                74
D4V4, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          12                88
  CLUS_2          21                13
  CLUS_3           2                56
  CLUS_4           1                22
D4V5, multiclass
D4V6, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           2                30
  CLUS_2          31                86
  CLUS_3           4                65
D4V7, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          17                41
  CLUS_2           1                31
  CLUS_3           5                77
  CLUS_4          14                33
D4V8, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           2                 6
  CLUS_2           7                88
  CLUS_3          28                88

Clustering(5) Variable = 7q gain
D5V1, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           2                 7
  CLUS_2           0                10
  CLUS_3           2                 6
D5V2, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           2                 7
  CLUS_2           2                 5
  CLUS_3           0                11
D5V3, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          10                84
  CLUS_2          34                16
  CLUS_3           7                69
D5V4, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          20                80
  CLUS_2          23                11
  CLUS_3           6                52
  CLUS_4           1                22
D5V5, multiclass
D5V6, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           4                28
  CLUS_2          38                79
  CLUS_3           8                61
D5V7, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          19                39
  CLUS_2           2                30
  CLUS_3          11                71
  CLUS_4          19                28
D5V8, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           2                 6
  CLUS_2          15                80
  CLUS_3          34                82

Clustering(6) Variable = 8p gain
D6V1, 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" 
D6V2, 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" 
D6V3, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          10                84
  CLUS_2           3                47
  CLUS_3           1                75
D6V4, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          10                90
  CLUS_2           2                32
  CLUS_3           1                57
  CLUS_4           1                22
D6V5, multiclass
D6V6, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           1                31
  CLUS_2          10               107
  CLUS_3           3                66
D6V7, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           8                50
  CLUS_2           0                32
  CLUS_3           3                79
  CLUS_4           3                44
D6V8, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           4                91
  CLUS_3          10               106

Clustering(7) Variable = 8q gain
D7V1, 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" 
D7V2, 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" 
D7V3, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          13                81
  CLUS_2           3                47
  CLUS_3           1                75
D7V4, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          13                87
  CLUS_2           2                32
  CLUS_3           1                57
  CLUS_4           1                22
D7V5, multiclass
D7V6, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           1                31
  CLUS_2          13               104
  CLUS_3           3                66
D7V7, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           9                49
  CLUS_2           1                31
  CLUS_3           3                79
  CLUS_4           4                43
D7V8, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           5                90
  CLUS_3          12               104

Clustering(8) Variable = 9p gain
D8V1, multiclass
D8V2, multiclass
D8V3, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           2                92
  CLUS_2           2                48
  CLUS_3           0                76
D8V4, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           3                97
  CLUS_2           1                33
  CLUS_3           0                58
  CLUS_4           0                23
D8V5, multiclass
D8V6, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           0                32
  CLUS_2           3               114
  CLUS_3           1                68
D8V7, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           1                57
  CLUS_2           0                32
  CLUS_3           2                80
  CLUS_4           1                46
D8V8, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           1                 7
  CLUS_2           2                93
  CLUS_3           1               115

Clustering(9) Variable = 9q gain
D9V1, multiclass
[1] "Remove cluster labels:" "9Q GAIN CNV"           
clus
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DH-5144        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
D9V2, multiclass
[1] "Remove cluster labels:" "9Q GAIN CNV"           
clus
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DH-5144        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
D9V3, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           2                92
  CLUS_2           4                46
  CLUS_3           0                76
D9V4, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           4                96
  CLUS_2           2                32
  CLUS_3           0                58
  CLUS_4           0                23
D9V5, multiclass
D9V6, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           0                32
  CLUS_2           5               112
  CLUS_3           1                68
D9V7, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           2                56
  CLUS_2           0                32
  CLUS_3           2                80
  CLUS_4           2                45
D9V8, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           1                 7
  CLUS_2           2                93
  CLUS_3           3               113

Clustering(10) Variable = 10p gain
D10V1, 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" 
D10V2, 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" 
D10V3, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           20                 74
  CLUS_2            0                 50
  CLUS_3            1                 75
D10V4, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           20                 80
  CLUS_2            0                 34
  CLUS_3            0                 58
  CLUS_4            1                 22
D10V5, multiclass
D10V6, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            0                 32
  CLUS_2           14                103
  CLUS_3            7                 62
D10V7, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            7                 51
  CLUS_2            2                 30
  CLUS_3            8                 74
  CLUS_4            4                 43
D10V8, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            0                  8
  CLUS_2           10                 85
  CLUS_3           11                105

Clustering(11) Variable = 11p gain
D11V1, 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" 
D11V2, 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" 
D11V3, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            3                 91
  CLUS_2            1                 49
  CLUS_3            5                 71
D11V4, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            4                 96
  CLUS_2            0                 34
  CLUS_3            5                 53
  CLUS_4            0                 23
D11V5, multiclass
D11V6, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            5                 27
  CLUS_2            4                113
  CLUS_3            0                 69
D11V7, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            3                 55
  CLUS_2            3                 29
  CLUS_3            1                 81
  CLUS_4            2                 45
D11V8, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            2                 93
  CLUS_3            7                109

Clustering(12) Variable = 11q gain
D12V1, 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" 
D12V2, 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" 
D12V3, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            7                 87
  CLUS_2            1                 49
  CLUS_3            6                 70
D12V4, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            8                 92
  CLUS_2            0                 34
  CLUS_3            5                 53
  CLUS_4            1                 22
D12V5, multiclass
D12V6, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            5                 27
  CLUS_2            6                111
  CLUS_3            3                 66
D12V7, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            4                 54
  CLUS_2            3                 29
  CLUS_3            4                 78
  CLUS_4            3                 44
D12V8, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            4                 91
  CLUS_3           10                106

Clustering(13) Variable = 12p gain
D13V1, 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" 
D13V2, 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" 
D13V3, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            9                 85
  CLUS_2            1                 49
  CLUS_3            1                 75
D13V4, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            9                 91
  CLUS_2            0                 34
  CLUS_3            1                 57
  CLUS_4            1                 22
D13V5, multiclass
D13V6, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            1                 31
  CLUS_2            9                108
  CLUS_3            1                 68
D13V7, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            5                 53
  CLUS_2            1                 31
  CLUS_3            1                 81
  CLUS_4            4                 43
D13V8, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            1                 94
  CLUS_3           10                106

Clustering(14) Variable = 12q gain
D14V1, multiclass
D14V2, multiclass
D14V3, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            3                 91
  CLUS_2            1                 49
  CLUS_3            1                 75
D14V4, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            4                 96
  CLUS_2            0                 34
  CLUS_3            1                 57
  CLUS_4            0                 23
D14V5, multiclass
D14V6, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            1                 31
  CLUS_2            4                113
  CLUS_3            0                 69
D14V7, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            2                 56
  CLUS_2            0                 32
  CLUS_3            0                 82
  CLUS_4            3                 44
D14V8, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            0                 95
  CLUS_3            5                111

Clustering(15) Variable = 18p gain
D15V1, 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" 
D15V2, 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" 
D15V3, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            2                 92
  CLUS_2            2                 48
  CLUS_3            0                 76
D15V4, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            3                 97
  CLUS_2            1                 33
  CLUS_3            0                 58
  CLUS_4            0                 23
D15V5, multiclass
D15V6, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            0                 32
  CLUS_2            4                113
  CLUS_3            0                 69
D15V7, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            2                 56
  CLUS_2            1                 31
  CLUS_3            1                 81
  CLUS_4            0                 47
D15V8, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            1                  7
  CLUS_2            1                 94
  CLUS_3            2                114

Clustering(16) Variable = 19p gain
D16V1, 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" 
D16V2, 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" 
D16V3, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            2                 92
  CLUS_2            9                 41
  CLUS_3            0                 76
D16V4, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            3                 97
  CLUS_2            8                 26
  CLUS_3            0                 58
  CLUS_4            0                 23
D16V5, multiclass
D16V6, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            0                 32
  CLUS_2           10                107
  CLUS_3            0                 69
D16V7, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            5                 53
  CLUS_2            0                 32
  CLUS_3            1                 81
  CLUS_4            5                 42
D16V8, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            1                  7
  CLUS_2            1                 94
  CLUS_3            9                107

Clustering(17) Variable = 19q gain
D17V1, 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" 
D17V2, 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" 
D17V3, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            2                 92
  CLUS_2            7                 43
  CLUS_3            0                 76
D17V4, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            2                 98
  CLUS_2            6                 28
  CLUS_3            0                 58
  CLUS_4            0                 23
D17V5, multiclass
D17V6, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            0                 32
  CLUS_2            9                108
  CLUS_3            0                 69
D17V7, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            3                 55
  CLUS_2            0                 32
  CLUS_3            1                 81
  CLUS_4            5                 42
D17V8, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            1                 94
  CLUS_3            8                108

Clustering(18) Variable = 20p gain
D18V1, 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" 
D18V2, 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" 
D18V3, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            4                 90
  CLUS_2           12                 38
  CLUS_3            1                 75
D18V4, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            6                 94
  CLUS_2           10                 24
  CLUS_3            1                 57
  CLUS_4            0                 23
D18V5, multiclass
D18V6, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            1                 31
  CLUS_2           12                105
  CLUS_3            3                 66
D18V7, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            6                 52
  CLUS_2            0                 32
  CLUS_3            3                 79
  CLUS_4            8                 39
D18V8, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            1                  7
  CLUS_2            4                 91
  CLUS_3           12                104

Clustering(19) Variable = 20q gain
D19V1, 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" 
D19V2, 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" 
D19V3, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            4                 90
  CLUS_2           11                 39
  CLUS_3            1                 75
D19V4, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            5                 95
  CLUS_2           10                 24
  CLUS_3            1                 57
  CLUS_4            0                 23
D19V5, multiclass
D19V6, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            1                 31
  CLUS_2           13                104
  CLUS_3            1                 68
D19V7, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            8                 50
  CLUS_2            0                 32
  CLUS_3            1                 81
  CLUS_4            7                 40
D19V8, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            1                  7
  CLUS_2            2                 93
  CLUS_3           13                103

Clustering(20) Variable = 21q gain
D20V1, multiclass
D20V2, multiclass
D20V3, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            0                 94
  CLUS_2            1                 49
  CLUS_3            2                 74
D20V4, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            1                 99
  CLUS_2            0                 34
  CLUS_3            2                 56
  CLUS_4            0                 23
D20V5, multiclass
D20V6, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            2                 30
  CLUS_2            1                116
  CLUS_3            0                 69
D20V7, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            1                 57
  CLUS_2            0                 32
  CLUS_3            1                 81
  CLUS_4            1                 46
D20V8, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            1                 94
  CLUS_3            2                114

Clustering(21) Variable = 1p loss
D21V1, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           0                 9
  CLUS_2           7                 3
  CLUS_3           2                 6
D21V2, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           0                 9
  CLUS_2           2                 5
  CLUS_3           7                 4
D21V3, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           0                94
  CLUS_2           0                50
  CLUS_3          67                 9
D21V4, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           0               100
  CLUS_2           0                34
  CLUS_3          58                 0
  CLUS_4           6                17
D21V5, multiclass
D21V6, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1          32                 0
  CLUS_2           4               113
  CLUS_3          31                38
D21V7, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           6                52
  CLUS_2          21                11
  CLUS_3          39                43
  CLUS_4           1                46
D21V8, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           3                 5
  CLUS_2          46                49
  CLUS_3          18                98

Clustering(22) Variable = 1q loss
D22V1, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0                 9
  CLUS_2           3                 7
  CLUS_3           0                 8
D22V2, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0                 9
  CLUS_2           0                 7
  CLUS_3           3                 8
D22V3, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0                94
  CLUS_2           0                50
  CLUS_3           9                67
D22V4, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0               100
  CLUS_2           0                34
  CLUS_3           9                49
  CLUS_4           0                23
D22V5, multiclass
D22V6, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           5                27
  CLUS_2           0               117
  CLUS_3           4                65
D22V7, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0                58
  CLUS_2           4                28
  CLUS_3           5                77
  CLUS_4           0                47
D22V8, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           6                89
  CLUS_3           3               113

Clustering(23) Variable = 2p loss
D23V1, multiclass
D23V2, multiclass
D23V3, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           1                93
  CLUS_2           1                49
  CLUS_3           2                74
D23V4, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           2                98
  CLUS_2           1                33
  CLUS_3           1                57
  CLUS_4           0                23
D23V5, multiclass
D23V6, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           1                31
  CLUS_2           3               114
  CLUS_3           0                69
D23V7, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           0                58
  CLUS_2           1                31
  CLUS_3           1                81
  CLUS_4           2                45
D23V8, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           1                 7
  CLUS_2           0                95
  CLUS_3           3               113

Clustering(24) Variable = 2q loss
D24V1, 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" 
D24V2, 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" 
D24V3, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           2                92
  CLUS_2           0                50
  CLUS_3           1                75
D24V4, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           2                98
  CLUS_2           0                34
  CLUS_3           1                57
  CLUS_4           0                23
D24V5, multiclass
D24V6, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1                31
  CLUS_2           2               115
  CLUS_3           0                69
D24V7, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           0                58
  CLUS_2           2                30
  CLUS_3           0                82
  CLUS_4           1                46
D24V8, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           1                94
  CLUS_3           2               114

Clustering(25) Variable = 3p loss
D25V1, 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" 
D25V2, 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" 
D25V3, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           3                91
  CLUS_2           0                50
  CLUS_3           1                75
D25V4, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           3                97
  CLUS_2           1                33
  CLUS_3           0                58
  CLUS_4           0                23
D25V5, multiclass
D25V6, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           0                32
  CLUS_2           4               113
  CLUS_3           0                69
D25V7, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           1                57
  CLUS_2           1                31
  CLUS_3           0                82
  CLUS_4           2                45
D25V8, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           1                94
  CLUS_3           3               113

Clustering(26) Variable = 3q loss
D26V1, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           1                 8
  CLUS_2           0                10
  CLUS_3           2                 6
D26V2, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           1                 8
  CLUS_2           1                 6
  CLUS_3           1                10
D26V3, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           7                87
  CLUS_2           1                49
  CLUS_3           1                75
D26V4, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           8                92
  CLUS_2           1                33
  CLUS_3           0                58
  CLUS_4           0                23
D26V5, multiclass
D26V6, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           0                32
  CLUS_2           7               110
  CLUS_3           2                67
D26V7, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           2                56
  CLUS_2           1                31
  CLUS_3           3                79
  CLUS_4           3                44
D26V8, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           4                91
  CLUS_3           5               111

Clustering(27) Variable = 4p loss
D27V1, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           0                 9
  CLUS_2           2                 8
  CLUS_3           2                 6
D27V2, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           0                 9
  CLUS_2           1                 6
  CLUS_3           3                 8
D27V3, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           2                92
  CLUS_2           1                49
  CLUS_3          12                64
D27V4, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           3                97
  CLUS_2           0                34
  CLUS_3          12                46
  CLUS_4           0                23
D27V5, multiclass
D27V6, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           7                25
  CLUS_2           2               115
  CLUS_3           6                63
D27V7, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           0                58
  CLUS_2           9                23
  CLUS_3           5                77
  CLUS_4           1                46
D27V8, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           9                86
  CLUS_3           6               110

Clustering(28) Variable = 4q loss
D28V1, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           1                 8
  CLUS_2           2                 8
  CLUS_3           2                 6
D28V2, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           1                 8
  CLUS_2           1                 6
  CLUS_3           3                 8
D28V3, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           8                86
  CLUS_2           1                49
  CLUS_3          15                61
D28V4, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           8                92
  CLUS_2           0                34
  CLUS_3          15                43
  CLUS_4           1                22
D28V5, multiclass
D28V6, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           9                23
  CLUS_2           7               110
  CLUS_3           7                62
D28V7, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           1                57
  CLUS_2          13                19
  CLUS_3           8                74
  CLUS_4           2                45
D28V8, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           2                 6
  CLUS_2          14                81
  CLUS_3           8               108

Clustering(29) Variable = 5p loss
D29V1, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           2                 7
  CLUS_2           2                 8
  CLUS_3           1                 7
D29V2, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           2                 7
  CLUS_2           0                 7
  CLUS_3           3                 8
D29V3, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           8                86
  CLUS_2           3                47
  CLUS_3           0                76
D29V4, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1          10                90
  CLUS_2           1                33
  CLUS_3           0                58
  CLUS_4           0                23
D29V5, multiclass
D29V6, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           0                32
  CLUS_2           8               109
  CLUS_3           3                66
D29V7, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           0                58
  CLUS_2           4                28
  CLUS_3           4                78
  CLUS_4           3                44
D29V8, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           1                 7
  CLUS_2           5                90
  CLUS_3           5               111

Clustering(30) Variable = 5q loss
D30V1, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           0                 9
  CLUS_2           2                 8
  CLUS_3           1                 7
D30V2, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           0                 9
  CLUS_2           0                 7
  CLUS_3           3                 8
D30V3, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           6                88
  CLUS_2           3                47
  CLUS_3           0                76
D30V4, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           8                92
  CLUS_2           1                33
  CLUS_3           0                58
  CLUS_4           0                23
D30V5, multiclass
D30V6, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           0                32
  CLUS_2           9               108
  CLUS_3           0                69
D30V7, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           0                58
  CLUS_2           2                30
  CLUS_3           1                81
  CLUS_4           6                41
D30V8, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           1                 7
  CLUS_2           2                93
  CLUS_3           6               110

Clustering(31) Variable = 6p loss
D31V1, multiclass
D31V2, multiclass
D31V3, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           2                92
  CLUS_2           4                46
  CLUS_3           1                75
D31V4, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           1                99
  CLUS_2           4                30
  CLUS_3           1                57
  CLUS_4           1                22
D31V5, multiclass
D31V6, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           1                31
  CLUS_2           4               113
  CLUS_3           2                67
D31V7, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           3                55
  CLUS_2           1                31
  CLUS_3           1                81
  CLUS_4           2                45
D31V8, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           1                 7
  CLUS_2           1                94
  CLUS_3           5               111

Clustering(32) Variable = 6q loss
D32V1, 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" 
D32V2, 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" 
D32V3, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           7                87
  CLUS_2          11                39
  CLUS_3           3                73
D32V4, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          12                88
  CLUS_2           7                27
  CLUS_3           1                57
  CLUS_4           1                22
D32V5, multiclass
D32V6, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           1                31
  CLUS_2          14               103
  CLUS_3           6                63
D32V7, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          10                48
  CLUS_2           2                30
  CLUS_3           6                76
  CLUS_4           3                44
D32V8, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           1                 7
  CLUS_2           6                89
  CLUS_3          14               102

Clustering(33) Variable = 8p loss
D33V1, 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" 
D33V2, 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" 
D33V3, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           1                93
  CLUS_2           2                48
  CLUS_3           0                76
D33V4, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           1                99
  CLUS_2           2                32
  CLUS_3           0                58
  CLUS_4           0                23
D33V5, multiclass
D33V6, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           0                32
  CLUS_2           2               115
  CLUS_3           1                68
D33V7, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           0                58
  CLUS_2           2                30
  CLUS_3           0                82
  CLUS_4           1                46
D33V8, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           1                94
  CLUS_3           2               114

Clustering(34) Variable = 9p loss
D34V1, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           1                 8
  CLUS_2           1                 9
  CLUS_3           3                 5
D34V2, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           1                 8
  CLUS_2           2                 5
  CLUS_3           2                 9
D34V3, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          13                81
  CLUS_2          17                33
  CLUS_3           8                68
D34V4, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          22                78
  CLUS_2           8                26
  CLUS_3           6                52
  CLUS_4           1                22
D34V5, multiclass
D34V6, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           5                27
  CLUS_2          25                92
  CLUS_3           8                61
D34V7, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           9                49
  CLUS_2           7                25
  CLUS_3          12                70
  CLUS_4          10                37
D34V8, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           1                 7
  CLUS_2          16                79
  CLUS_3          21                95

Clustering(35) Variable = 9q loss
D35V1, multiclass
D35V2, multiclass
D35V3, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           1                93
  CLUS_2           0                50
  CLUS_3           5                71
D35V4, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           1                99
  CLUS_2           0                34
  CLUS_3           5                53
  CLUS_4           0                23
D35V5, multiclass
D35V6, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           4                28
  CLUS_2           0               117
  CLUS_3           2                67
D35V7, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           0                58
  CLUS_2           4                28
  CLUS_3           2                80
  CLUS_4           0                47
D35V8, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           4                91
  CLUS_3           2               114

Clustering(36) Variable = 10p loss
D36V1, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            0                  9
  CLUS_2            1                  9
  CLUS_3            2                  6
D36V2, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            0                  9
  CLUS_2            2                  5
  CLUS_3            1                 10
D36V3, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            1                 93
  CLUS_2           27                 23
  CLUS_3            3                 73
D36V4, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            1                 99
  CLUS_2           26                  8
  CLUS_3            3                 55
  CLUS_4            0                 23
D36V5, multiclass
D36V6, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            1                 31
  CLUS_2           25                 92
  CLUS_3            4                 65
D36V7, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1           14                 44
  CLUS_2            3                 29
  CLUS_3            5                 77
  CLUS_4            9                 38
D36V8, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            2                  6
  CLUS_2            5                 90
  CLUS_3           24                 92

Clustering(37) Variable = 10q loss
D37V1, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            0                  9
  CLUS_2            1                  9
  CLUS_3            2                  6
D37V2, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            0                  9
  CLUS_2            2                  5
  CLUS_3            1                 10
D37V3, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            2                 92
  CLUS_2           27                 23
  CLUS_3            3                 73
D37V4, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            2                 98
  CLUS_2           26                  8
  CLUS_3            3                 55
  CLUS_4            0                 23
D37V5, multiclass
D37V6, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            1                 31
  CLUS_2           26                 91
  CLUS_3            4                 65
D37V7, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           14                 44
  CLUS_2            3                 29
  CLUS_3            5                 77
  CLUS_4           10                 37
D37V8, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            2                  6
  CLUS_2            6                 89
  CLUS_3           24                 92

Clustering(38) Variable = 11p loss
D38V1, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            2                  7
  CLUS_2            1                  9
  CLUS_3            1                  7
D38V2, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            2                  7
  CLUS_2            0                  7
  CLUS_3            2                  9
D38V3, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1           15                 79
  CLUS_2            4                 46
  CLUS_3            1                 75
D38V4, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1           17                 83
  CLUS_2            2                 32
  CLUS_3            0                 58
  CLUS_4            1                 22
D38V5, multiclass
D38V6, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            0                 32
  CLUS_2           17                100
  CLUS_3            3                 66
D38V7, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            3                 55
  CLUS_2            1                 31
  CLUS_3            5                 77
  CLUS_4           11                 36
D38V8, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            1                  7
  CLUS_2            6                 89
  CLUS_3           13                103

Clustering(39) Variable = 11q loss
D39V1, 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" 
D39V2, 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" 
D39V3, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            0                 94
  CLUS_2            4                 46
  CLUS_3            0                 76
D39V4, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            2                 98
  CLUS_2            2                 32
  CLUS_3            0                 58
  CLUS_4            0                 23
D39V5, multiclass
D39V6, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            0                 32
  CLUS_2            4                113
  CLUS_3            0                 69
D39V7, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            1                 57
  CLUS_2            0                 32
  CLUS_3            1                 81
  CLUS_4            2                 45
D39V8, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            1                  7
  CLUS_2            0                 95
  CLUS_3            3                113

Clustering(40) Variable = 12q loss
D40V1, 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" 
D40V2, 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" 
D40V3, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            7                 87
  CLUS_2            0                 50
  CLUS_3            1                 75
D40V4, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            7                 93
  CLUS_2            0                 34
  CLUS_3            1                 57
  CLUS_4            0                 23
D40V5, multiclass
D40V6, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            0                 32
  CLUS_2            6                111
  CLUS_3            2                 67
D40V7, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            0                 58
  CLUS_2            1                 31
  CLUS_3            3                 79
  CLUS_4            4                 43
D40V8, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            4                 91
  CLUS_3            4                112

Clustering(41) Variable = 13q loss
D41V1, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            2                  7
  CLUS_2            2                  8
  CLUS_3            1                  7
D41V2, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            2                  7
  CLUS_2            0                  7
  CLUS_3            3                  8
D41V3, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           10                 84
  CLUS_2            8                 42
  CLUS_3           10                 66
D41V4, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           15                 85
  CLUS_2            6                 28
  CLUS_3            7                 51
  CLUS_4            0                 23
D41V5, multiclass
D41V6, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            4                 28
  CLUS_2           17                100
  CLUS_3            6                 63
D41V7, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            7                 51
  CLUS_2            6                 26
  CLUS_3            9                 73
  CLUS_4            6                 41
D41V8, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            1                  7
  CLUS_2           10                 85
  CLUS_3           17                 99

Clustering(42) Variable = 14q loss
D42V1, 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" 
D42V2, 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" 
D42V3, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            5                 89
  CLUS_2           13                 37
  CLUS_3            6                 70
D42V4, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            8                 92
  CLUS_2           11                 23
  CLUS_3            5                 53
  CLUS_4            0                 23
D42V5, multiclass
D42V6, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            2                 30
  CLUS_2           16                101
  CLUS_3            6                 63
D42V7, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           12                 46
  CLUS_2            3                 29
  CLUS_3            6                 76
  CLUS_4            3                 44
D42V8, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            1                  7
  CLUS_2            6                 89
  CLUS_3           17                 99

Clustering(43) Variable = 15q loss
D43V1, 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" 
D43V2, 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" 
D43V3, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            1                 93
  CLUS_2            2                 48
  CLUS_3            9                 67
D43V4, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            2                 98
  CLUS_2            1                 33
  CLUS_3            9                 49
  CLUS_4            0                 23
D43V5, multiclass
D43V6, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            6                 26
  CLUS_2            3                114
  CLUS_3            3                 66
D43V7, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            4                 54
  CLUS_2            3                 29
  CLUS_3            4                 78
  CLUS_4            1                 46
D43V8, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            5                 90
  CLUS_3            7                109

Clustering(44) Variable = 16q loss
D44V1, 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" 
D44V2, 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" 
D44V3, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            3                 91
  CLUS_2            2                 48
  CLUS_3            1                 75
D44V4, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            3                 97
  CLUS_2            3                 31
  CLUS_3            0                 58
  CLUS_4            0                 23
D44V5, multiclass
D44V6, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            0                 32
  CLUS_2            5                112
  CLUS_3            1                 68
D44V7, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            3                 55
  CLUS_2            0                 32
  CLUS_3            2                 80
  CLUS_4            1                 46
D44V8, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            2                 93
  CLUS_3            4                112

Clustering(45) Variable = 18p loss
D45V1, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            1                  8
  CLUS_2            3                  7
  CLUS_3            0                  8
D45V2, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            1                  8
  CLUS_2            0                  7
  CLUS_3            3                  8
D45V3, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            3                 91
  CLUS_2            4                 46
  CLUS_3            8                 68
D45V4, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            4                 96
  CLUS_2            3                 31
  CLUS_3            8                 50
  CLUS_4            0                 23
D45V5, multiclass
D45V6, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            5                 27
  CLUS_2            6                111
  CLUS_3            4                 65
D45V7, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            3                 55
  CLUS_2            6                 26
  CLUS_3            4                 78
  CLUS_4            2                 45
D45V8, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            3                 92
  CLUS_3           12                104

Clustering(46) Variable = 18q loss
D46V1, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            0                  9
  CLUS_2            3                  7
  CLUS_3            0                  8
D46V2, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            0                  9
  CLUS_2            0                  7
  CLUS_3            3                  8
D46V3, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            1                 93
  CLUS_2            5                 45
  CLUS_3           10                 66
D46V4, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            3                 97
  CLUS_2            3                 31
  CLUS_3           10                 48
  CLUS_4            0                 23
D46V5, multiclass
D46V6, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            6                 26
  CLUS_2            5                112
  CLUS_3            5                 64
D46V7, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            3                 55
  CLUS_2            6                 26
  CLUS_3            5                 77
  CLUS_4            2                 45
D46V8, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            4                 91
  CLUS_3           12                104

Clustering(47) Variable = 19p loss
D47V1, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                  8
  CLUS_2            4                  6
  CLUS_3            1                  7
D47V2, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                  8
  CLUS_2            0                  7
  CLUS_3            5                  6
D47V3, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                 93
  CLUS_2            3                 47
  CLUS_3            6                 70
D47V4, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            3                 97
  CLUS_2            1                 33
  CLUS_3            6                 52
  CLUS_4            0                 23
D47V5, multiclass
D47V6, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            4                 28
  CLUS_2            2                115
  CLUS_3            4                 65
D47V7, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                 57
  CLUS_2            5                 27
  CLUS_3            3                 79
  CLUS_4            1                 46
D47V8, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            5                 90
  CLUS_3            5                111

Clustering(48) Variable = 19q loss
D48V1, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            3                  6
  CLUS_2            7                  3
  CLUS_3            3                  5
D48V2, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            3                  6
  CLUS_2            2                  5
  CLUS_3            8                  3
D48V3, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            2                 92
  CLUS_2            3                 47
  CLUS_3           71                  5
D48V4, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            8                 92
  CLUS_2            2                 32
  CLUS_3           57                  1
  CLUS_4            6                 17
D48V5, multiclass
D48V6, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1           32                  0
  CLUS_2            9                108
  CLUS_3           35                 34
D48V7, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            7                 51
  CLUS_2           23                  9
  CLUS_3           42                 40
  CLUS_4            4                 43
D48V8, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            2                  6
  CLUS_2           51                 44
  CLUS_3           23                 93

Clustering(49) Variable = 21q loss
D49V1, 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" 
D49V2, 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" 
D49V3, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            3                 91
  CLUS_2            3                 47
  CLUS_3            2                 74
D49V4, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            5                 95
  CLUS_2            2                 32
  CLUS_3            1                 57
  CLUS_4            0                 23
D49V5, multiclass
D49V6, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            0                 32
  CLUS_2            6                111
  CLUS_3            2                 67
D49V7, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            1                 57
  CLUS_2            0                 32
  CLUS_3            2                 80
  CLUS_4            5                 42
D49V8, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            1                  7
  CLUS_2            0                 95
  CLUS_3            7                109

Clustering(50) Variable = 22q loss
D50V1, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            1                  8
  CLUS_2            1                  9
  CLUS_3            1                  7
D50V2, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            1                  8
  CLUS_2            0                  7
  CLUS_3            2                  9
D50V3, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            4                 90
  CLUS_2           11                 39
  CLUS_3            0                 76
D50V4, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            6                 94
  CLUS_2            9                 25
  CLUS_3            0                 58
  CLUS_4            0                 23
D50V5, multiclass
D50V6, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            0                 32
  CLUS_2           12                105
  CLUS_3            2                 67
D50V7, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            7                 51
  CLUS_2            2                 30
  CLUS_3            3                 79
  CLUS_4            3                 44
D50V8, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            0                  8
  CLUS_2            4                 91
  CLUS_3           11                105

Clustering(51) Variable = Xq loss
D51V1, multiclass
D51V2, multiclass
D51V3, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           4                90
  CLUS_2           2                48
  CLUS_3           0                76
D51V4, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           5                95
  CLUS_2           1                33
  CLUS_3           0                58
  CLUS_4           0                23
D51V5, multiclass
D51V6, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           0                32
  CLUS_2           6               111
  CLUS_3           0                69
D51V7, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           3                55
  CLUS_2           0                32
  CLUS_3           0                82
  CLUS_4           3                44
D51V8, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           0                 8
  CLUS_2           1                94
  CLUS_3           5               111
                     V1                      V2                      V3 
            "MRNA_CNMF"    "MRNA_CHIERARCHICAL"               "CN_CNMF" 
                     V4                      V5                      V6 
     "METHLYATION_CNMF"          "MRNASEQ_CNMF" "MRNASEQ_CHIERARCHICAL" 
                     V7                      V8 
          "MIRSEQ_CNMF"  "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
