
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/PRAD-TP/4430225/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/PRAD-TP/4430172/PRAD-TP.transferedmergedcluster.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=PRAD-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=PRAD-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=248, in cluster file=197, common to both=197
[1] "Reduce the number of clustering variables from 80 to 32."
[1]  32 197
[1] "1p gain"
[1] 3
      1P GAIN CNV 1P GAIN WILD-TYPE 
                3               194 
      1P GAIN CNV 1P GAIN WILD-TYPE 
                3               194 
[1] "1q gain"
[1] 3
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
                5               192 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
                5               192 
[1] "3p gain"
[1] 3
      3P GAIN CNV 3P GAIN WILD-TYPE 
                5               192 
      3P GAIN CNV 3P GAIN WILD-TYPE 
                5               192 
[1] "3q gain"
[1] 3
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                7               190 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                7               190 
[1] "7p gain"
[1] 3
      7P GAIN CNV 7P GAIN WILD-TYPE 
               17               180 
      7P GAIN CNV 7P GAIN WILD-TYPE 
               17               180 
[1] "7q gain"
[1] 3
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               16               181 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               16               181 
[1] "8p gain"
[1] 3
      8P GAIN CNV 8P GAIN WILD-TYPE 
               11               186 
      8P GAIN CNV 8P GAIN WILD-TYPE 
               11               186 
[1] "8q gain"
[1] 3
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               24               173 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               24               173 
[1] "9p gain"
[1] 3
      9P GAIN CNV 9P GAIN WILD-TYPE 
                3               194 
      9P GAIN CNV 9P GAIN WILD-TYPE 
                3               194 
[1] "9q gain"
[1] 3
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                8               189 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                8               189 
[1] "10q gain"
[1] 3
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 4                193 
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 4                193 
[1] "12q gain"
[1] 3
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 3                194 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 3                194 
[1] "16p gain"
[1] 3
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 3                194 
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 3                194 
[1] "16q gain"
[1] 3
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                 3                194 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                 3                194 
[1] "5q loss"
[1] 3
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
                5               192 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
                5               192 
[1] "6q loss"
[1] 3
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
                9               188 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
                9               188 
[1] "8p loss"
[1] 3
      8P LOSS CNV 8P LOSS WILD-TYPE 
               48               149 
      8P LOSS CNV 8P LOSS WILD-TYPE 
               48               149 
[1] "8q loss"
[1] 3
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                4               193 
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                4               193 
[1] "10p loss"
[1] 3
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 7                190 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 7                190 
[1] "10q loss"
[1] 3
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                 7                190 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                 7                190 
[1] "12p loss"
[1] 3
      12P LOSS CNV 12P LOSS WILD-TYPE 
                11                186 
      12P LOSS CNV 12P LOSS WILD-TYPE 
                11                186 
[1] "13q loss"
[1] 3
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                15                182 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                15                182 
[1] "15q loss"
[1] 3
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                 3                194 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                 3                194 
[1] "16p loss"
[1] 3
      16P LOSS CNV 16P LOSS WILD-TYPE 
                 4                193 
      16P LOSS CNV 16P LOSS WILD-TYPE 
                 4                193 
[1] "16q loss"
[1] 3
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                28                169 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                28                169 
[1] "17p loss"
[1] 3
      17P LOSS CNV 17P LOSS WILD-TYPE 
                24                173 
      17P LOSS CNV 17P LOSS WILD-TYPE 
                24                173 
[1] "18p loss"
[1] 3
      18P LOSS CNV 18P LOSS WILD-TYPE 
                19                178 
      18P LOSS CNV 18P LOSS WILD-TYPE 
                19                178 
[1] "18q loss"
[1] 3
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                26                171 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                26                171 
[1] "20p loss"
[1] 3
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 5                192 
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 5                192 
[1] "21q loss"
[1] 3
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 5                192 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 5                192 
[1] "22q loss"
[1] 3
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                 5                192 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                 5                192 
[1] "Xq loss"
[1] 3
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                3               194 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                3               194 
[1] "data2feature, selection="
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 10 rows and 197 columns.

Variable 1:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_MATURE_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 197 columns, 0 survival variables, and 10 non-survival variables.
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain
D1V1, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           0                28
  CLUS_2           0               108
  CLUS_3           3                58
D1V2, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           3                54
  CLUS_2           0                65
  CLUS_3           0                75
D1V3, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           0                41
  CLUS_2           1                55
  CLUS_3           2                55
D1V4, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           0                51
  CLUS_2           2                56
  CLUS_3           1                44
D1V5, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           3                64
  CLUS_2           0                60
  CLUS_3           0                67
D1V6, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           2                47
  CLUS_2           1                67
  CLUS_3           0                77
D1V7, multiclass
D1V8, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           1                33
  CLUS_2           1                20
  CLUS_3           1                73
  CLUS_4           0                67
D1V9, multiclass
D1V10, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           2                76
  CLUS_2           1                91
  CLUS_3           0                26

Clustering(2) Variable = 1q gain
D2V1, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           0                28
  CLUS_2           0               108
  CLUS_3           5                56
D2V2, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           3                54
  CLUS_2           0                65
  CLUS_3           2                73
D2V3, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           0                41
  CLUS_2           1                55
  CLUS_3           4                53
D2V4, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           0                51
  CLUS_2           4                54
  CLUS_3           1                44
D2V5, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           3                64
  CLUS_2           0                60
  CLUS_3           2                65
D2V6, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           2                47
  CLUS_2           3                65
  CLUS_3           0                77
D2V7, multiclass
D2V8, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           1                33
  CLUS_2           1                20
  CLUS_3           3                71
  CLUS_4           0                67
D2V9, multiclass
D2V10, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           3                75
  CLUS_2           2                90
  CLUS_3           0                26

Clustering(3) Variable = 3p gain
D3V1, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           1                27
  CLUS_2           2               106
  CLUS_3           2                59
D3V2, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           3                54
  CLUS_2           1                64
  CLUS_3           1                74
D3V3, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           0                41
  CLUS_2           1                55
  CLUS_3           4                53
D3V4, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           0                51
  CLUS_2           4                54
  CLUS_3           1                44
D3V5, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           4                63
  CLUS_2           0                60
  CLUS_3           1                66
D3V6, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           2                47
  CLUS_2           3                65
  CLUS_3           0                77
D3V7, multiclass
D3V8, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           2                32
  CLUS_2           2                19
  CLUS_3           1                73
  CLUS_4           0                67
D3V9, multiclass
D3V10, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           3                75
  CLUS_2           2                90
  CLUS_3           0                26

Clustering(4) Variable = 3q gain
D4V1, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           2                26
  CLUS_2           2               106
  CLUS_3           3                58
D4V2, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           4                53
  CLUS_2           1                64
  CLUS_3           2                73
D4V3, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           0                41
  CLUS_2           1                55
  CLUS_3           5                52
D4V4, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           0                51
  CLUS_2           5                53
  CLUS_3           1                44
D4V5, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           6                61
  CLUS_2           0                60
  CLUS_3           1                66
D4V6, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           3                46
  CLUS_2           4                64
  CLUS_3           0                77
D4V7, multiclass
D4V8, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           3                31
  CLUS_2           3                18
  CLUS_3           1                73
  CLUS_4           0                67
D4V9, multiclass
D4V10, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           2                76
  CLUS_2           3                89
  CLUS_3           2                24

Clustering(5) Variable = 7p gain
D5V1, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           2                26
  CLUS_2           0               108
  CLUS_3          15                46
D5V2, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           7                50
  CLUS_2           1                64
  CLUS_3           9                66
D5V3, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           4                37
  CLUS_2           2                54
  CLUS_3          10                47
D5V4, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           3                48
  CLUS_2          10                48
  CLUS_3           3                42
D5V5, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           8                59
  CLUS_2           1                59
  CLUS_3           8                59
D5V6, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           3                46
  CLUS_2          11                57
  CLUS_3           3                74
D5V7, multiclass
D5V8, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           1                33
  CLUS_2           8                13
  CLUS_3           5                69
  CLUS_4           3                64
D5V9, multiclass
D5V10, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           6                72
  CLUS_2           6                86
  CLUS_3           5                21

Clustering(6) Variable = 7q gain
D6V1, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           2                26
  CLUS_2           0               108
  CLUS_3          14                47
D6V2, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           8                49
  CLUS_2           1                64
  CLUS_3           7                68
D6V3, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           4                37
  CLUS_2           2                54
  CLUS_3           9                48
D6V4, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           3                48
  CLUS_2           9                49
  CLUS_3           3                42
D6V5, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           8                59
  CLUS_2           1                59
  CLUS_3           7                60
D6V6, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           4                45
  CLUS_2           9                59
  CLUS_3           3                74
D6V7, multiclass
D6V8, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           1                33
  CLUS_2           7                14
  CLUS_3           5                69
  CLUS_4           3                64
D6V9, multiclass
D6V10, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           6                72
  CLUS_2           6                86
  CLUS_3           4                22

Clustering(7) Variable = 8p gain
D7V1, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           0                28
  CLUS_2           0               108
  CLUS_3          11                50
D7V2, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           6                51
  CLUS_2           1                64
  CLUS_3           4                71
D7V3, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           0                41
  CLUS_2           0                56
  CLUS_3           8                49
D7V4, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           0                51
  CLUS_2           8                50
  CLUS_3           0                45
D7V5, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           8                59
  CLUS_2           1                59
  CLUS_3           2                65
D7V6, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           4                45
  CLUS_2           6                62
  CLUS_3           1                76
D7V7, multiclass
D7V8, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           1                33
  CLUS_2           5                16
  CLUS_3           4                70
  CLUS_4           1                66
D7V9, multiclass
D7V10, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           3                75
  CLUS_2           5                87
  CLUS_3           3                23

Clustering(8) Variable = 8q gain
D8V1, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           2                26
  CLUS_2           2               106
  CLUS_3          20                41
D8V2, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          10                47
  CLUS_2           4                61
  CLUS_3          10                65
D8V3, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           0                41
  CLUS_2           4                52
  CLUS_3          14                43
D8V4, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           0                51
  CLUS_2          14                44
  CLUS_3           4                41
D8V5, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          15                52
  CLUS_2           3                57
  CLUS_3           6                61
D8V6, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           7                42
  CLUS_2          14                54
  CLUS_3           3                74
D8V7, multiclass
D8V8, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           2                32
  CLUS_2           9                12
  CLUS_3          11                63
  CLUS_4           1                66
D8V9, multiclass
D8V10, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           5                73
  CLUS_2          12                80
  CLUS_3           6                20

Clustering(9) Variable = 9p gain
D9V1, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           0                28
  CLUS_2           0               108
  CLUS_3           3                58
D9V2, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           2                55
  CLUS_2           0                65
  CLUS_3           1                74
D9V3, multiclass
[1] "Remove cluster labels:" "9P GAIN CNV"           
clus
      9P GAIN CNV 9P GAIN WILD-TYPE 
                2               152 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5748 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752        TCGA-CH-5753 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762        TCGA-CH-5763 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766        TCGA-CH-5767 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5772 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790        TCGA-CH-5791 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5495 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503        TCGA-EJ-5504 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517        TCGA-EJ-5518 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522        TCGA-EJ-5524 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527        TCGA-EJ-5530 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542        TCGA-EJ-7115 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-7125        TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-7321        TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-7781        TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-7785        TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7791 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-8468        TCGA-EJ-8469        TCGA-EJ-8470        TCGA-EJ-8474 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-A46B        TCGA-EJ-A46D        TCGA-EJ-A46E        TCGA-EJ-A46F 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-A46G        TCGA-FC-7708        TCGA-FC-A4JI        TCGA-G9-6329 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G9-6338        TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6351 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6494 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G9-6496        TCGA-G9-6499        TCGA-G9-7510        TCGA-G9-7521 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G9-7522        TCGA-G9-7523        TCGA-G9-7525        TCGA-H9-7775 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-HC-7077        TCGA-HC-7079        TCGA-HC-7081        TCGA-HC-7210 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7232 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7740        TCGA-HC-7744 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-HC-7748        TCGA-HC-8264        TCGA-HI-7168        TCGA-HI-7169 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-HI-7170        TCGA-HI-7171        TCGA-J4-8198        TCGA-J9-A52C 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-J9-A52E        TCGA-KC-A4BL        TCGA-KC-A4BN        TCGA-KC-A4BO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KC-A4BR        TCGA-KC-A4BV        TCGA-KK-A59Y        TCGA-KK-A59Z 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
D9V4, multiclass
[1] "Remove cluster labels:" "9P GAIN CNV"           
clus
      9P GAIN CNV 9P GAIN WILD-TYPE 
                2               152 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5748 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752        TCGA-CH-5753 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762        TCGA-CH-5763 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766        TCGA-CH-5767 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5772 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790        TCGA-CH-5791 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5495 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503        TCGA-EJ-5504 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517        TCGA-EJ-5518 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522        TCGA-EJ-5524 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527        TCGA-EJ-5530 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542        TCGA-EJ-7115 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-7125        TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-7321        TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-7781        TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-7785        TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7791 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-8468        TCGA-EJ-8469        TCGA-EJ-8470        TCGA-EJ-8474 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-A46B        TCGA-EJ-A46D        TCGA-EJ-A46E        TCGA-EJ-A46F 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EJ-A46G        TCGA-FC-7708        TCGA-FC-A4JI        TCGA-G9-6329 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G9-6338        TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6351 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6494 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G9-6496        TCGA-G9-6499        TCGA-G9-7510        TCGA-G9-7521 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G9-7522        TCGA-G9-7523        TCGA-G9-7525        TCGA-H9-7775 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-HC-7077        TCGA-HC-7079        TCGA-HC-7081        TCGA-HC-7210 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7232 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7740        TCGA-HC-7744 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-HC-7748        TCGA-HC-8264        TCGA-HI-7168        TCGA-HI-7169 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-HI-7170        TCGA-HI-7171        TCGA-J4-8198        TCGA-J9-A52C 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-J9-A52E        TCGA-KC-A4BL        TCGA-KC-A4BN        TCGA-KC-A4BO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KC-A4BR        TCGA-KC-A4BV        TCGA-KK-A59Y        TCGA-KK-A59Z 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
D9V5, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           2                65
  CLUS_2           0                60
  CLUS_3           1                66
D9V6, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           0                49
  CLUS_2           3                65
  CLUS_3           0                77
D9V7, multiclass
D9V8, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           1                33
  CLUS_2           0                21
  CLUS_3           2                72
  CLUS_4           0                67
D9V9, multiclass
D9V10, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           1                77
  CLUS_2           2                90
  CLUS_3           0                26

Clustering(10) Variable = 9q gain
D10V1, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           0                28
  CLUS_2           1               107
  CLUS_3           7                54
D10V2, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           3                54
  CLUS_2           0                65
  CLUS_3           5                70
D10V3, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           1                40
  CLUS_2           0                56
  CLUS_3           5                52
D10V4, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           1                50
  CLUS_2           5                53
  CLUS_3           0                45
D10V5, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           4                63
  CLUS_2           0                60
  CLUS_3           4                63
D10V6, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           2                47
  CLUS_2           5                63
  CLUS_3           1                76
D10V7, multiclass
D10V8, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           0                34
  CLUS_2           3                18
  CLUS_3           2                72
  CLUS_4           3                64
D10V9, multiclass
D10V10, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           3                75
  CLUS_2           3                89
  CLUS_3           2                24

Clustering(11) Variable = 10q gain
D11V1, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            0                 28
  CLUS_2            1                107
  CLUS_3            3                 58
D11V2, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            2                 55
  CLUS_2            0                 65
  CLUS_3            2                 73
D11V3, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            0                 41
  CLUS_2            0                 56
  CLUS_3            3                 54
D11V4, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            0                 51
  CLUS_2            3                 55
  CLUS_3            0                 45
D11V5, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            3                 64
  CLUS_2            0                 60
  CLUS_3            1                 66
D11V6, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            1                 48
  CLUS_2            3                 65
  CLUS_3            0                 77
D11V7, multiclass
D11V8, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            0                 34
  CLUS_2            2                 19
  CLUS_3            2                 72
  CLUS_4            0                 67
D11V9, multiclass
D11V10, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            1                 77
  CLUS_2            2                 90
  CLUS_3            1                 25

Clustering(12) Variable = 12q gain
D12V1, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            0                 28
  CLUS_2            1                107
  CLUS_3            2                 59
D12V2, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            2                 55
  CLUS_2            1                 64
  CLUS_3            0                 75
D12V3, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            1                 40
  CLUS_2            0                 56
  CLUS_3            2                 55
D12V4, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            1                 50
  CLUS_2            1                 57
  CLUS_3            1                 44
D12V5, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            2                 65
  CLUS_2            1                 59
  CLUS_3            0                 67
D12V6, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            1                 48
  CLUS_2            1                 67
  CLUS_3            1                 76
D12V7, multiclass
D12V8, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            0                 34
  CLUS_2            1                 20
  CLUS_3            1                 73
  CLUS_4            1                 66
D12V9, multiclass
D12V10, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            2                 76
  CLUS_2            1                 91
  CLUS_3            0                 26

Clustering(13) Variable = 16p gain
D13V1, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            0                 28
  CLUS_2            0                108
  CLUS_3            3                 58
D13V2, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            2                 55
  CLUS_2            0                 65
  CLUS_3            1                 74
D13V3, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            0                 41
  CLUS_2            1                 55
  CLUS_3            2                 55
D13V4, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            0                 51
  CLUS_2            2                 56
  CLUS_3            1                 44
D13V5, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            1                 66
  CLUS_2            0                 60
  CLUS_3            2                 65
D13V6, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            0                 49
  CLUS_2            3                 65
  CLUS_3            0                 77
D13V7, multiclass
D13V8, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            0                 34
  CLUS_2            1                 20
  CLUS_3            1                 73
  CLUS_4            1                 66
D13V9, multiclass
D13V10, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            2                 76
  CLUS_2            1                 91
  CLUS_3            0                 26

Clustering(14) Variable = 16q gain
D14V1, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            0                 28
  CLUS_2            0                108
  CLUS_3            3                 58
D14V2, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            2                 55
  CLUS_2            0                 65
  CLUS_3            1                 74
D14V3, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            0                 41
  CLUS_2            1                 55
  CLUS_3            2                 55
D14V4, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            0                 51
  CLUS_2            2                 56
  CLUS_3            1                 44
D14V5, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            1                 66
  CLUS_2            0                 60
  CLUS_3            2                 65
D14V6, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            0                 49
  CLUS_2            3                 65
  CLUS_3            0                 77
D14V7, multiclass
D14V8, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            0                 34
  CLUS_2            1                 20
  CLUS_3            1                 73
  CLUS_4            1                 66
D14V9, multiclass
D14V10, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            2                 76
  CLUS_2            1                 91
  CLUS_3            0                 26

Clustering(15) Variable = 5q loss
D15V1, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           0                28
  CLUS_2           0               108
  CLUS_3           5                56
D15V2, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           4                53
  CLUS_2           0                65
  CLUS_3           1                74
D15V3, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           0                41
  CLUS_2           1                55
  CLUS_3           3                54
D15V4, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           0                51
  CLUS_2           3                55
  CLUS_3           1                44
D15V5, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           4                63
  CLUS_2           0                60
  CLUS_3           1                66
D15V6, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           1                48
  CLUS_2           4                64
  CLUS_3           0                77
D15V7, multiclass
D15V8, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           0                34
  CLUS_2           3                18
  CLUS_3           2                72
  CLUS_4           0                67
D15V9, multiclass
D15V10, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           2                76
  CLUS_2           3                89
  CLUS_3           0                26

Clustering(16) Variable = 6q loss
D16V1, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           2                26
  CLUS_2           0               108
  CLUS_3           7                54
D16V2, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           4                53
  CLUS_2           0                65
  CLUS_3           5                70
D16V3, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           2                39
  CLUS_2           1                55
  CLUS_3           4                53
D16V4, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           2                49
  CLUS_2           4                54
  CLUS_3           1                44
D16V5, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           5                62
  CLUS_2           0                60
  CLUS_3           4                63
D16V6, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           4                45
  CLUS_2           5                63
  CLUS_3           0                77
D16V7, multiclass
D16V8, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           3                31
  CLUS_2           2                19
  CLUS_3           3                71
  CLUS_4           1                66
D16V9, multiclass
D16V10, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           3                75
  CLUS_2           4                88
  CLUS_3           2                24

Clustering(17) Variable = 8p loss
D17V1, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           1                27
  CLUS_2          26                82
  CLUS_3          21                40
D17V2, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          11                46
  CLUS_2           5                60
  CLUS_3          32                43
D17V3, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           8                33
  CLUS_2          16                40
  CLUS_3          16                41
D17V4, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          14                37
  CLUS_2          16                42
  CLUS_3          10                35
D17V5, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          12                55
  CLUS_2           8                52
  CLUS_3          28                39
D17V6, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          10                39
  CLUS_2          28                40
  CLUS_3          10                67
D17V7, multiclass
D17V8, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           7                27
  CLUS_2           6                15
  CLUS_3          22                52
  CLUS_4          13                54
D17V9, multiclass
D17V10, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          22                56
  CLUS_2          24                68
  CLUS_3           2                24

Clustering(18) Variable = 8q loss
D18V1, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           0                28
  CLUS_2           1               107
  CLUS_3           3                58
D18V2, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           1                56
  CLUS_2           0                65
  CLUS_3           3                72
D18V3, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           0                41
  CLUS_2           2                54
  CLUS_3           2                55
D18V4, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           1                50
  CLUS_2           2                56
  CLUS_3           1                44
D18V5, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           1                66
  CLUS_2           0                60
  CLUS_3           3                64
D18V6, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           1                48
  CLUS_2           3                65
  CLUS_3           0                77
D18V7, multiclass
D18V8, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           0                34
  CLUS_2           1                20
  CLUS_3           1                73
  CLUS_4           2                65
D18V9, multiclass
D18V10, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           3                75
  CLUS_2           1                91
  CLUS_3           0                26

Clustering(19) Variable = 10p loss
D19V1, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            0                 28
  CLUS_2            1                107
  CLUS_3            6                 55
D19V2, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            4                 53
  CLUS_2            0                 65
  CLUS_3            3                 72
D19V3, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            0                 41
  CLUS_2            1                 55
  CLUS_3            5                 52
D19V4, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            0                 51
  CLUS_2            5                 53
  CLUS_3            1                 44
D19V5, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            3                 64
  CLUS_2            0                 60
  CLUS_3            4                 63
D19V6, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            2                 47
  CLUS_2            5                 63
  CLUS_3            0                 77
D19V7, multiclass
D19V8, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            3                 31
  CLUS_2            2                 19
  CLUS_3            2                 72
  CLUS_4            0                 67
D19V9, multiclass
D19V10, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            2                 76
  CLUS_2            3                 89
  CLUS_3            2                 24

Clustering(20) Variable = 10q loss
D20V1, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            0                 28
  CLUS_2            1                107
  CLUS_3            6                 55
D20V2, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            3                 54
  CLUS_2            1                 64
  CLUS_3            3                 72
D20V3, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            0                 41
  CLUS_2            1                 55
  CLUS_3            4                 53
D20V4, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            0                 51
  CLUS_2            4                 54
  CLUS_3            1                 44
D20V5, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            2                 65
  CLUS_2            1                 59
  CLUS_3            4                 63
D20V6, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            1                 48
  CLUS_2            5                 63
  CLUS_3            1                 76
D20V7, multiclass
D20V8, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            1                 33
  CLUS_2            2                 19
  CLUS_3            2                 72
  CLUS_4            2                 65
D20V9, multiclass
D20V10, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            2                 76
  CLUS_2            3                 89
  CLUS_3            2                 24

Clustering(21) Variable = 12p loss
D21V1, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            0                 28
  CLUS_2            3                105
  CLUS_3            8                 53
D21V2, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            2                 55
  CLUS_2            1                 64
  CLUS_3            8                 67
D21V3, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            1                 40
  CLUS_2            1                 55
  CLUS_3            5                 52
D21V4, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            2                 49
  CLUS_2            4                 54
  CLUS_3            1                 44
D21V5, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            1                 66
  CLUS_2            2                 58
  CLUS_3            8                 59
D21V6, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            0                 49
  CLUS_2            8                 60
  CLUS_3            3                 74
D21V7, multiclass
D21V8, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            1                 33
  CLUS_2            2                 19
  CLUS_3            2                 72
  CLUS_4            6                 61
D21V9, multiclass
D21V10, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            6                 72
  CLUS_2            4                 88
  CLUS_3            1                 25

Clustering(22) Variable = 13q loss
D22V1, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            3                 25
  CLUS_2            0                108
  CLUS_3           12                 49
D22V2, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            6                 51
  CLUS_2            1                 64
  CLUS_3            8                 67
D22V3, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            5                 36
  CLUS_2            0                 56
  CLUS_3            8                 49
D22V4, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            5                 46
  CLUS_2            8                 50
  CLUS_3            0                 45
D22V5, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            7                 60
  CLUS_2            0                 60
  CLUS_3            8                 59
D22V6, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            3                 46
  CLUS_2           10                 58
  CLUS_3            2                 75
D22V7, multiclass
D22V8, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            2                 32
  CLUS_2            4                 17
  CLUS_3            3                 71
  CLUS_4            5                 62
D22V9, multiclass
D22V10, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            6                 72
  CLUS_2            5                 87
  CLUS_3            3                 23

Clustering(23) Variable = 15q loss
D23V1, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            0                 28
  CLUS_2            0                108
  CLUS_3            3                 58
D23V2, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            3                 54
  CLUS_2            0                 65
  CLUS_3            0                 75
D23V3, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            0                 41
  CLUS_2            1                 55
  CLUS_3            2                 55
D23V4, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            0                 51
  CLUS_2            2                 56
  CLUS_3            1                 44
D23V5, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            3                 64
  CLUS_2            0                 60
  CLUS_3            0                 67
D23V6, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            2                 47
  CLUS_2            1                 67
  CLUS_3            0                 77
D23V7, multiclass
D23V8, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            0                 34
  CLUS_2            2                 19
  CLUS_3            1                 73
  CLUS_4            0                 67
D23V9, multiclass
D23V10, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            1                 77
  CLUS_2            1                 91
  CLUS_3            1                 25

Clustering(24) Variable = 16p loss
D24V1, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            0                 28
  CLUS_2            0                108
  CLUS_3            4                 57
D24V2, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            4                 53
  CLUS_2            0                 65
  CLUS_3            0                 75
D24V3, multiclass
[1] "Remove cluster labels:" "16P LOSS CNV"          
clus
      16P LOSS CNV 16P LOSS WILD-TYPE 
                 2                152 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5748         TCGA-CH-5750 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CH-5752         TCGA-CH-5753         TCGA-CH-5754 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CH-5761         TCGA-CH-5762         TCGA-CH-5763 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CH-5764         TCGA-CH-5765         TCGA-CH-5766 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CH-5767         TCGA-CH-5768         TCGA-CH-5769 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CH-5771         TCGA-CH-5772         TCGA-CH-5788 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CH-5789         TCGA-CH-5790         TCGA-CH-5791 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CH-5792         TCGA-CH-5794         TCGA-EJ-5494 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-5495         TCGA-EJ-5496         TCGA-EJ-5497 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-5498         TCGA-EJ-5499         TCGA-EJ-5501 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-5502         TCGA-EJ-5503         TCGA-EJ-5504 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-5505         TCGA-EJ-5506         TCGA-EJ-5507 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-5508         TCGA-EJ-5509         TCGA-EJ-5510 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-5511         TCGA-EJ-5512         TCGA-EJ-5514 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-5515         TCGA-EJ-5516         TCGA-EJ-5517 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-5518         TCGA-EJ-5519         TCGA-EJ-5521 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-5522         TCGA-EJ-5524         TCGA-EJ-5525 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-5526         TCGA-EJ-5527         TCGA-EJ-5530 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-5531         TCGA-EJ-5532         TCGA-EJ-5542 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7125         TCGA-EJ-7314 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7321 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7793         TCGA-EJ-7794 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-7797         TCGA-EJ-8468         TCGA-EJ-8469 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-8470         TCGA-EJ-8474         TCGA-EJ-A46B 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-A46D         TCGA-EJ-A46E         TCGA-EJ-A46F 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-A46G         TCGA-FC-7708         TCGA-FC-A4JI 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6338         TCGA-G9-6342 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6351         TCGA-G9-6353 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G9-6356         TCGA-G9-6361         TCGA-G9-6362 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G9-6363         TCGA-G9-6364         TCGA-G9-6365 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G9-6366         TCGA-G9-6367         TCGA-G9-6370 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G9-6371         TCGA-G9-6373         TCGA-G9-6377 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G9-6378         TCGA-G9-6384         TCGA-G9-6494 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-G9-7510 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G9-7521         TCGA-G9-7522         TCGA-G9-7523 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G9-7525         TCGA-H9-7775         TCGA-HC-7077 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HC-7079         TCGA-HC-7081         TCGA-HC-7210 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HC-7211         TCGA-HC-7212         TCGA-HC-7213 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HC-7232         TCGA-HC-7233         TCGA-HC-7736 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HC-7740         TCGA-HC-7744         TCGA-HC-7748 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HC-8264         TCGA-HI-7168         TCGA-HI-7169 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HI-7170         TCGA-HI-7171         TCGA-J4-8198 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-J9-A52C         TCGA-J9-A52E         TCGA-KC-A4BL 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KC-A4BN         TCGA-KC-A4BO         TCGA-KC-A4BR 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KC-A4BV         TCGA-KK-A59Y 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
D24V4, multiclass
[1] "Remove cluster labels:" "16P LOSS CNV"          
clus
      16P LOSS CNV 16P LOSS WILD-TYPE 
                 2                152 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5748         TCGA-CH-5750 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CH-5752         TCGA-CH-5753         TCGA-CH-5754 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CH-5761         TCGA-CH-5762         TCGA-CH-5763 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CH-5764         TCGA-CH-5765         TCGA-CH-5766 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CH-5767         TCGA-CH-5768         TCGA-CH-5769 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CH-5771         TCGA-CH-5772         TCGA-CH-5788 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CH-5789         TCGA-CH-5790         TCGA-CH-5791 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CH-5792         TCGA-CH-5794         TCGA-EJ-5494 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-5495         TCGA-EJ-5496         TCGA-EJ-5497 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-5498         TCGA-EJ-5499         TCGA-EJ-5501 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-5502         TCGA-EJ-5503         TCGA-EJ-5504 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-5505         TCGA-EJ-5506         TCGA-EJ-5507 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-5508         TCGA-EJ-5509         TCGA-EJ-5510 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-5511         TCGA-EJ-5512         TCGA-EJ-5514 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-5515         TCGA-EJ-5516         TCGA-EJ-5517 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-5518         TCGA-EJ-5519         TCGA-EJ-5521 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-5522         TCGA-EJ-5524         TCGA-EJ-5525 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-5526         TCGA-EJ-5527         TCGA-EJ-5530 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-5531         TCGA-EJ-5532         TCGA-EJ-5542 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7125         TCGA-EJ-7314 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7321 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7793         TCGA-EJ-7794 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-7797         TCGA-EJ-8468         TCGA-EJ-8469 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-8470         TCGA-EJ-8474         TCGA-EJ-A46B 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-A46D         TCGA-EJ-A46E         TCGA-EJ-A46F 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EJ-A46G         TCGA-FC-7708         TCGA-FC-A4JI 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6338         TCGA-G9-6342 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6351         TCGA-G9-6353 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G9-6356         TCGA-G9-6361         TCGA-G9-6362 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G9-6363         TCGA-G9-6364         TCGA-G9-6365 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G9-6366         TCGA-G9-6367         TCGA-G9-6370 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G9-6371         TCGA-G9-6373         TCGA-G9-6377 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G9-6378         TCGA-G9-6384         TCGA-G9-6494 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-G9-7510 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G9-7521         TCGA-G9-7522         TCGA-G9-7523 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G9-7525         TCGA-H9-7775         TCGA-HC-7077 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HC-7079         TCGA-HC-7081         TCGA-HC-7210 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HC-7211         TCGA-HC-7212         TCGA-HC-7213 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HC-7232         TCGA-HC-7233         TCGA-HC-7736 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HC-7740         TCGA-HC-7744         TCGA-HC-7748 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HC-8264         TCGA-HI-7168         TCGA-HI-7169 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HI-7170         TCGA-HI-7171         TCGA-J4-8198 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-J9-A52C         TCGA-J9-A52E         TCGA-KC-A4BL 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KC-A4BN         TCGA-KC-A4BO         TCGA-KC-A4BR 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KC-A4BV         TCGA-KK-A59Y 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
D24V5, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            4                 63
  CLUS_2            0                 60
  CLUS_3            0                 67
D24V6, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            2                 47
  CLUS_2            2                 66
  CLUS_3            0                 77
D24V7, multiclass
D24V8, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            0                 34
  CLUS_2            2                 19
  CLUS_3            1                 73
  CLUS_4            0                 67
D24V9, multiclass
D24V10, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            0                 78
  CLUS_2            1                 91
  CLUS_3            2                 24

Clustering(25) Variable = 16q loss
D25V1, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            1                 27
  CLUS_2            4                104
  CLUS_3           23                 38
D25V2, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           11                 46
  CLUS_2            2                 63
  CLUS_3           15                 60
D25V3, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            4                 37
  CLUS_2            7                 49
  CLUS_3           11                 46
D25V4, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            5                 46
  CLUS_2           13                 45
  CLUS_3            4                 41
D25V5, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           12                 55
  CLUS_2            3                 57
  CLUS_3           13                 54
D25V6, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            7                 42
  CLUS_2           17                 51
  CLUS_3            4                 73
D25V7, multiclass
D25V8, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            2                 32
  CLUS_2            9                 12
  CLUS_3           12                 62
  CLUS_4            4                 63
D25V9, multiclass
D25V10, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            8                 70
  CLUS_2           13                 79
  CLUS_3            6                 20

Clustering(26) Variable = 17p loss
D26V1, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            0                 28
  CLUS_2            5                103
  CLUS_3           19                 42
D26V2, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           11                 46
  CLUS_2            2                 63
  CLUS_3           11                 64
D26V3, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            1                 40
  CLUS_2            6                 50
  CLUS_3           12                 45
D26V4, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            2                 49
  CLUS_2           12                 46
  CLUS_3            5                 40
D26V5, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           10                 57
  CLUS_2            2                 58
  CLUS_3           12                 55
D26V6, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            5                 44
  CLUS_2           16                 52
  CLUS_3            3                 74
D26V7, multiclass
D26V8, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            3                 31
  CLUS_2            7                 14
  CLUS_3            7                 67
  CLUS_4            7                 60
D26V9, multiclass
D26V10, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           12                 66
  CLUS_2            8                 84
  CLUS_3            4                 22

Clustering(27) Variable = 18p loss
D27V1, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            1                 27
  CLUS_2            5                103
  CLUS_3           13                 48
D27V2, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            8                 49
  CLUS_2            3                 62
  CLUS_3            8                 67
D27V3, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            1                 40
  CLUS_2            2                 54
  CLUS_3            9                 48
D27V4, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            1                 50
  CLUS_2            9                 49
  CLUS_3            2                 43
D27V5, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            6                 61
  CLUS_2            4                 56
  CLUS_3            9                 58
D27V6, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            3                 46
  CLUS_2           11                 57
  CLUS_3            5                 72
D27V7, multiclass
D27V8, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            2                 32
  CLUS_2            3                 18
  CLUS_3           11                 63
  CLUS_4            3                 64
D27V9, multiclass
D27V10, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            4                 74
  CLUS_2           14                 78
  CLUS_3            1                 25

Clustering(28) Variable = 18q loss
D28V1, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            1                 27
  CLUS_2            7                101
  CLUS_3           18                 43
D28V2, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            8                 49
  CLUS_2            5                 60
  CLUS_3           13                 62
D28V3, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            2                 39
  CLUS_2            2                 54
  CLUS_3           12                 45
D28V4, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            2                 49
  CLUS_2           12                 46
  CLUS_3            2                 43
D28V5, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            9                 58
  CLUS_2            4                 56
  CLUS_3           13                 54
D28V6, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            5                 44
  CLUS_2           15                 53
  CLUS_3            6                 71
D28V7, multiclass
D28V8, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            2                 32
  CLUS_2            6                 15
  CLUS_3           13                 61
  CLUS_4            5                 62
D28V9, multiclass
D28V10, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            8                 70
  CLUS_2           16                 76
  CLUS_3            2                 24

Clustering(29) Variable = 20p loss
D29V1, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            1                 27
  CLUS_2            2                106
  CLUS_3            2                 59
D29V2, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            4                 53
  CLUS_2            0                 65
  CLUS_3            1                 74
D29V3, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            1                 40
  CLUS_2            3                 53
  CLUS_3            1                 56
D29V4, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            2                 49
  CLUS_2            1                 57
  CLUS_3            2                 43
D29V5, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            4                 63
  CLUS_2            0                 60
  CLUS_3            1                 66
D29V6, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            3                 46
  CLUS_2            1                 67
  CLUS_3            1                 76
D29V7, multiclass
D29V8, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            3                 31
  CLUS_2            1                 20
  CLUS_3            1                 73
  CLUS_4            0                 67
D29V9, multiclass
D29V10, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            4                 74
  CLUS_2            1                 91
  CLUS_3            0                 26

Clustering(30) Variable = 21q loss
D30V1, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            0                 28
  CLUS_2            1                107
  CLUS_3            4                 57
D30V2, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            2                 55
  CLUS_2            0                 65
  CLUS_3            3                 72
D30V3, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            1                 40
  CLUS_2            0                 56
  CLUS_3            2                 55
D30V4, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            1                 50
  CLUS_2            2                 56
  CLUS_3            0                 45
D30V5, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            1                 66
  CLUS_2            0                 60
  CLUS_3            4                 63
D30V6, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            0                 49
  CLUS_2            4                 64
  CLUS_3            1                 76
D30V7, multiclass
D30V8, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            0                 34
  CLUS_2            2                 19
  CLUS_3            1                 73
  CLUS_4            2                 65
D30V9, multiclass
D30V10, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            2                 76
  CLUS_2            2                 90
  CLUS_3            1                 25

Clustering(31) Variable = 22q loss
D31V1, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            1                 27
  CLUS_2            0                108
  CLUS_3            4                 57
D31V2, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            2                 55
  CLUS_2            0                 65
  CLUS_3            3                 72
D31V3, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            1                 40
  CLUS_2            2                 54
  CLUS_3            1                 56
D31V4, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            1                 50
  CLUS_2            1                 57
  CLUS_3            2                 43
D31V5, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            2                 65
  CLUS_2            0                 60
  CLUS_3            3                 64
D31V6, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            2                 47
  CLUS_2            3                 65
  CLUS_3            0                 77
D31V7, multiclass
D31V8, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            1                 33
  CLUS_2            0                 21
  CLUS_3            2                 72
  CLUS_4            2                 65
D31V9, multiclass
D31V10, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            2                 76
  CLUS_2            3                 89
  CLUS_3            0                 26

Clustering(32) Variable = Xq loss
D32V1, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           1                27
  CLUS_2           0               108
  CLUS_3           2                59
D32V2, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           3                54
  CLUS_2           0                65
  CLUS_3           0                75
D32V3, multiclass
[1] "Remove cluster labels:" "XQ LOSS CNV"           
clus
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                2               152 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5748 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752        TCGA-CH-5753 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762        TCGA-CH-5763 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766        TCGA-CH-5767 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5772 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790        TCGA-CH-5791 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5495 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503        TCGA-EJ-5504 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-7115        TCGA-EJ-7125        TCGA-EJ-7314        TCGA-EJ-7315 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7328        TCGA-EJ-7330 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-7331        TCGA-EJ-7781        TCGA-EJ-7782        TCGA-EJ-7783 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-7784        TCGA-EJ-7785        TCGA-EJ-7786        TCGA-EJ-7788 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-7791        TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-7797        TCGA-EJ-8468        TCGA-EJ-8469        TCGA-EJ-8470 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-8474        TCGA-EJ-A46B        TCGA-EJ-A46D        TCGA-EJ-A46E 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-A46F        TCGA-EJ-A46G        TCGA-FC-7708        TCGA-FC-A4JI 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G9-6329        TCGA-G9-6338        TCGA-G9-6342        TCGA-G9-6343 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G9-6351        TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G9-6362        TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6370        TCGA-G9-6371 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499        TCGA-G9-7510 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G9-7521        TCGA-G9-7522        TCGA-G9-7523        TCGA-G9-7525 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7077        TCGA-HC-7079        TCGA-HC-7081 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-HC-7210        TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7740 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-HC-7744        TCGA-HC-7748        TCGA-HC-8264        TCGA-HI-7168 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171        TCGA-J4-8198 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-J9-A52C        TCGA-J9-A52E        TCGA-KC-A4BL        TCGA-KC-A4BN 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KC-A4BO        TCGA-KC-A4BR        TCGA-KC-A4BV        TCGA-KK-A59Y 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D32V4, multiclass
[1] "Remove cluster labels:" "XQ LOSS CNV"           
clus
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                2               152 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5748 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752        TCGA-CH-5753 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762        TCGA-CH-5763 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766        TCGA-CH-5767 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5772 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790        TCGA-CH-5791 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5495 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503        TCGA-EJ-5504 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-7115        TCGA-EJ-7125        TCGA-EJ-7314        TCGA-EJ-7315 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7328        TCGA-EJ-7330 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-7331        TCGA-EJ-7781        TCGA-EJ-7782        TCGA-EJ-7783 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-7784        TCGA-EJ-7785        TCGA-EJ-7786        TCGA-EJ-7788 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-7791        TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-7797        TCGA-EJ-8468        TCGA-EJ-8469        TCGA-EJ-8470 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-8474        TCGA-EJ-A46B        TCGA-EJ-A46D        TCGA-EJ-A46E 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EJ-A46F        TCGA-EJ-A46G        TCGA-FC-7708        TCGA-FC-A4JI 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G9-6329        TCGA-G9-6338        TCGA-G9-6342        TCGA-G9-6343 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G9-6351        TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G9-6362        TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6370        TCGA-G9-6371 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499        TCGA-G9-7510 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G9-7521        TCGA-G9-7522        TCGA-G9-7523        TCGA-G9-7525 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7077        TCGA-HC-7079        TCGA-HC-7081 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-HC-7210        TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7740 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-HC-7744        TCGA-HC-7748        TCGA-HC-8264        TCGA-HI-7168 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171        TCGA-J4-8198 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-J9-A52C        TCGA-J9-A52E        TCGA-KC-A4BL        TCGA-KC-A4BN 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-KC-A4BO        TCGA-KC-A4BR        TCGA-KC-A4BV        TCGA-KK-A59Y 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D32V5, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           3                64
  CLUS_2           0                60
  CLUS_3           0                67
D32V6, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           2                47
  CLUS_2           1                67
  CLUS_3           0                77
D32V7, multiclass
D32V8, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           0                34
  CLUS_2           1                20
  CLUS_3           1                73
  CLUS_4           1                66
D32V9, multiclass
D32V10, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           0                78
  CLUS_2           2                90
  CLUS_3           1                25
                           V1                            V2 
                    "CN_CNMF"            "METHLYATION_CNMF" 
                           V3                            V4 
                  "RPPA_CNMF"          "RPPA_CHIERARCHICAL" 
                           V5                            V6 
               "MRNASEQ_CNMF"       "MRNASEQ_CHIERARCHICAL" 
                           V7                            V8 
                "MIRSEQ_CNMF"        "MIRSEQ_CHIERARCHICAL" 
                           V9                           V10 
         "MIRSEQ_MATURE_CNMF" "MIRSEQ_MATURE_CHIERARCHICAL" 
> q(save="no")
