
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/KIRC-TP/3472602/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/KIRC-TP/3536964/KIRC-TP.transferedmergedcluster.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=KIRC-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=KIRC-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=513, in cluster file=504, common to both=504
[1] "Reduce the number of clustering variables from 80 to 71."
[1]  71 504
[1] "1p gain"
[1] 3
      1P GAIN CNV 1P GAIN WILD-TYPE 
                5               499 
      1P GAIN CNV 1P GAIN WILD-TYPE 
                5               499 
[1] "1q gain"
[1] 3
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
               32               472 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
               32               472 
[1] "2p gain"
[1] 3
      2P GAIN CNV 2P GAIN WILD-TYPE 
               49               455 
      2P GAIN CNV 2P GAIN WILD-TYPE 
               49               455 
[1] "2q gain"
[1] 3
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
               50               454 
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
               50               454 
[1] "3p gain"
[1] 3
      3P GAIN CNV 3P GAIN WILD-TYPE 
                7               497 
      3P GAIN CNV 3P GAIN WILD-TYPE 
                7               497 
[1] "3q gain"
[1] 3
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               29               475 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               29               475 
[1] "4p gain"
[1] 3
      4P GAIN CNV 4P GAIN WILD-TYPE 
                8               496 
      4P GAIN CNV 4P GAIN WILD-TYPE 
                8               496 
[1] "4q gain"
[1] 3
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                8               496 
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                8               496 
[1] "5p gain"
[1] 3
      5P GAIN CNV 5P GAIN WILD-TYPE 
              143               361 
      5P GAIN CNV 5P GAIN WILD-TYPE 
              143               361 
[1] "5q gain"
[1] 3
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
              159               345 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
              159               345 
[1] "6p gain"
[1] 3
      6P GAIN CNV 6P GAIN WILD-TYPE 
                6               498 
      6P GAIN CNV 6P GAIN WILD-TYPE 
                6               498 
[1] "6q gain"
[1] 3
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                5               499 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                5               499 
[1] "7p gain"
[1] 3
      7P GAIN CNV 7P GAIN WILD-TYPE 
              128               376 
      7P GAIN CNV 7P GAIN WILD-TYPE 
              128               376 
[1] "7q gain"
[1] 3
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
              130               374 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
              130               374 
[1] "8p gain"
[1] 3
      8P GAIN CNV 8P GAIN WILD-TYPE 
               16               488 
      8P GAIN CNV 8P GAIN WILD-TYPE 
               16               488 
[1] "8q gain"
[1] 3
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               36               468 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               36               468 
[1] "9p gain"
[1] 3
      9P GAIN CNV 9P GAIN WILD-TYPE 
                8               496 
      9P GAIN CNV 9P GAIN WILD-TYPE 
                8               496 
[1] "9q gain"
[1] 3
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                8               496 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                8               496 
[1] "10p gain"
[1] 3
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 6                498 
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 6                498 
[1] "10q gain"
[1] 3
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 4                500 
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 4                500 
[1] "11p gain"
[1] 3
      11P GAIN CNV 11P GAIN WILD-TYPE 
                17                487 
      11P GAIN CNV 11P GAIN WILD-TYPE 
                17                487 
[1] "11q gain"
[1] 3
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                15                489 
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                15                489 
[1] "12p gain"
[1] 3
      12P GAIN CNV 12P GAIN WILD-TYPE 
                80                424 
      12P GAIN CNV 12P GAIN WILD-TYPE 
                80                424 
[1] "12q gain"
[1] 3
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                81                423 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                81                423 
[1] "13q gain"
[1] 3
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                14                490 
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                14                490 
[1] "14q gain"
[1] 3
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 5                499 
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 5                499 
[1] "15q gain"
[1] 3
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                14                490 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                14                490 
[1] "16p gain"
[1] 3
      16P GAIN CNV 16P GAIN WILD-TYPE 
                68                436 
      16P GAIN CNV 16P GAIN WILD-TYPE 
                68                436 
[1] "16q gain"
[1] 3
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                61                443 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                61                443 
[1] "17p gain"
[1] 3
      17P GAIN CNV 17P GAIN WILD-TYPE 
                16                488 
      17P GAIN CNV 17P GAIN WILD-TYPE 
                16                488 
[1] "17q gain"
[1] 3
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                22                482 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                22                482 
[1] "18p gain"
[1] 3
      18P GAIN CNV 18P GAIN WILD-TYPE 
                18                486 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                18                486 
[1] "18q gain"
[1] 3
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                18                486 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                18                486 
[1] "19p gain"
[1] 3
      19P GAIN CNV 19P GAIN WILD-TYPE 
                25                479 
      19P GAIN CNV 19P GAIN WILD-TYPE 
                25                479 
[1] "19q gain"
[1] 3
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                28                476 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                28                476 
[1] "20p gain"
[1] 3
      20P GAIN CNV 20P GAIN WILD-TYPE 
                67                437 
      20P GAIN CNV 20P GAIN WILD-TYPE 
                67                437 
[1] "20q gain"
[1] 3
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                69                435 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                69                435 
[1] "21q gain"
[1] 3
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                35                469 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                35                469 
[1] "22q gain"
[1] 3
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                25                479 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                25                479 
[1] "Xq gain"
[1] 3
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                9               495 
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                9               495 
[1] "1p loss"
[1] 3
      1P LOSS CNV 1P LOSS WILD-TYPE 
               32               472 
      1P LOSS CNV 1P LOSS WILD-TYPE 
               32               472 
[1] "1q loss"
[1] 3
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
               20               484 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
               20               484 
[1] "2p loss"
[1] 3
      2P LOSS CNV 2P LOSS WILD-TYPE 
               10               494 
      2P LOSS CNV 2P LOSS WILD-TYPE 
               10               494 
[1] "2q loss"
[1] 3
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
               11               493 
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
               11               493 
[1] "3p loss"
[1] 3
      3P LOSS CNV 3P LOSS WILD-TYPE 
              311               193 
      3P LOSS CNV 3P LOSS WILD-TYPE 
              311               193 
[1] "3q loss"
[1] 3
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
               74               430 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
               74               430 
[1] "4p loss"
[1] 3
      4P LOSS CNV 4P LOSS WILD-TYPE 
               35               469 
      4P LOSS CNV 4P LOSS WILD-TYPE 
               35               469 
[1] "4q loss"
[1] 3
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               28               476 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               28               476 
[1] "6p loss"
[1] 3
      6P LOSS CNV 6P LOSS WILD-TYPE 
               59               445 
      6P LOSS CNV 6P LOSS WILD-TYPE 
               59               445 
[1] "6q loss"
[1] 3
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               85               419 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               85               419 
[1] "8p loss"
[1] 3
      8P LOSS CNV 8P LOSS WILD-TYPE 
               99               405 
      8P LOSS CNV 8P LOSS WILD-TYPE 
               99               405 
[1] "8q loss"
[1] 3
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
               40               464 
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
               40               464 
[1] "9p loss"
[1] 3
      9P LOSS CNV 9P LOSS WILD-TYPE 
               89               415 
      9P LOSS CNV 9P LOSS WILD-TYPE 
               89               415 
[1] "9q loss"
[1] 3
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
               94               410 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
               94               410 
[1] "10p loss"
[1] 3
      10P LOSS CNV 10P LOSS WILD-TYPE 
                32                472 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                32                472 
[1] "10q loss"
[1] 3
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                48                456 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                48                456 
[1] "11p loss"
[1] 3
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 5                499 
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 5                499 
[1] "11q loss"
[1] 3
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 7                497 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 7                497 
[1] "13q loss"
[1] 3
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                31                473 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                31                473 
[1] "14q loss"
[1] 3
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
               162                342 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
               162                342 
[1] "15q loss"
[1] 3
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                12                492 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                12                492 
[1] "16q loss"
[1] 3
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 6                498 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 6                498 
[1] "17p loss"
[1] 3
      17P LOSS CNV 17P LOSS WILD-TYPE 
                26                478 
      17P LOSS CNV 17P LOSS WILD-TYPE 
                26                478 
[1] "17q loss"
[1] 3
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                12                492 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                12                492 
[1] "18p loss"
[1] 3
      18P LOSS CNV 18P LOSS WILD-TYPE 
                46                458 
      18P LOSS CNV 18P LOSS WILD-TYPE 
                46                458 
[1] "18q loss"
[1] 3
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                48                456 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                48                456 
[1] "19p loss"
[1] 3
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 4                500 
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 4                500 
[1] "20p loss"
[1] 3
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 6                498 
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 6                498 
[1] "21q loss"
[1] 3
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                34                470 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                34                470 
[1] "22q loss"
[1] 3
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                12                492 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                12                492 
[1] "Xq loss"
[1] 3
      XQ LOSS CNV XQ LOSS WILD-TYPE 
               10               494 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
               10               494 
[1] "data2feature, selection="
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 12 rows and 504 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'RPPA_CNMF':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 504 columns, 0 survival variables, and 12 non-survival variables.
MRNA_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=6, 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=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain
D1V1, multiclass
[1] "Remove cluster labels:" "1P GAIN CNV"           
clus
      1P GAIN CNV 1P GAIN WILD-TYPE 
                2                68 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3374 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3456 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778        TCGA-B2-3923 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099        TCGA-B2-4102 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151        TCGA-B8-4154 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161        TCGA-BP-4162 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167        TCGA-CJ-4634 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638        TCGA-CJ-4639 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643        TCGA-CJ-4644 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
D1V2, multiclass
[1] "Remove cluster labels:" "1P GAIN CNV"           
clus
      1P GAIN CNV 1P GAIN WILD-TYPE 
                2                68 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3374 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3456 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778        TCGA-B2-3923 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099        TCGA-B2-4102 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151        TCGA-B8-4154 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161        TCGA-BP-4162 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167        TCGA-CJ-4634 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638        TCGA-CJ-4639 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643        TCGA-CJ-4644 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
D1V3, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           4               160
  CLUS_2           1               215
  CLUS_3           0               124
D1V4, multiclass
[1] "Remove cluster labels:" "1P GAIN CNV"           
clus
      1P GAIN CNV 1P GAIN WILD-TYPE 
                1               288 
       TCGA-A3-3357        TCGA-A3-3358        TCGA-A3-3367        TCGA-A3-3370 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3373        TCGA-A3-3376        TCGA-A3-3385        TCGA-A3-3387 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AK-3425        TCGA-AK-3428        TCGA-AK-3431        TCGA-AK-3433 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AK-3434        TCGA-AK-3440        TCGA-AK-3445        TCGA-AK-3450 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AK-3453        TCGA-AK-3454        TCGA-AK-3458        TCGA-AK-3460 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AK-3461        TCGA-B0-4688        TCGA-B0-4690        TCGA-B0-4691 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4693        TCGA-B0-4694        TCGA-B0-4696        TCGA-B0-4697 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4698        TCGA-B0-4699        TCGA-B0-4700        TCGA-B0-4701 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4703        TCGA-B0-4706        TCGA-B0-4707        TCGA-B0-4710 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4712        TCGA-B0-4713        TCGA-B0-4714        TCGA-B0-4718 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4810        TCGA-B0-4811        TCGA-B0-4813        TCGA-B0-4814 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4815        TCGA-B0-4816        TCGA-B0-4817        TCGA-B0-4818 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4819        TCGA-B0-4821        TCGA-B0-4822        TCGA-B0-4823 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4824        TCGA-B0-4827        TCGA-B0-4828        TCGA-B0-4841 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4842        TCGA-B0-4843        TCGA-B0-4844        TCGA-B0-4845 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4846        TCGA-B0-4847        TCGA-B0-4848        TCGA-B0-4849 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4852        TCGA-B0-4945        TCGA-B0-5080        TCGA-B0-5092 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5094        TCGA-B0-5095        TCGA-B0-5096        TCGA-B0-5097 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5098        TCGA-B0-5099        TCGA-B0-5100        TCGA-B0-5102 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5104        TCGA-B0-5106        TCGA-B0-5107        TCGA-B0-5108 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5110        TCGA-B0-5113        TCGA-B0-5115        TCGA-B0-5116 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5117        TCGA-B0-5119        TCGA-B0-5120        TCGA-B0-5121 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5399        TCGA-B0-5400        TCGA-B0-5402        TCGA-B0-5690 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5691        TCGA-B0-5692        TCGA-B0-5693        TCGA-B0-5694 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5695        TCGA-B0-5696        TCGA-B0-5697        TCGA-B0-5698 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5699        TCGA-B0-5701        TCGA-B0-5702        TCGA-B0-5703 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5705        TCGA-B0-5706        TCGA-B0-5709        TCGA-B0-5710 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5711        TCGA-B0-5712        TCGA-B0-5713        TCGA-B0-5812 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B2-4101        TCGA-B2-5633        TCGA-B2-5635        TCGA-B2-5639 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B2-5641        TCGA-B2-A4SR        TCGA-B4-5377        TCGA-B4-5378 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835        TCGA-B4-5836 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844        TCGA-B8-4146 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B8-4153        TCGA-B8-4621        TCGA-B8-4622        TCGA-B8-5158 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B8-5159        TCGA-B8-5162        TCGA-B8-5163        TCGA-B8-5164 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B8-5165        TCGA-B8-5545        TCGA-B8-5546        TCGA-B8-5549 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B8-5550        TCGA-B8-5551        TCGA-B8-5552        TCGA-B8-5553 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B8-A54D        TCGA-B8-A54E        TCGA-B8-A54F        TCGA-B8-A54G 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4177        TCGA-BP-4760        TCGA-BP-4770        TCGA-BP-4782 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4795        TCGA-BP-4801        TCGA-BP-4993        TCGA-BP-5010 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-5168        TCGA-BP-5169        TCGA-BP-5170        TCGA-BP-5173 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-5174        TCGA-BP-5175        TCGA-BP-5176        TCGA-BP-5177 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-5178        TCGA-BP-5180        TCGA-BP-5181        TCGA-BP-5182 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-5183        TCGA-BP-5184        TCGA-BP-5185        TCGA-BP-5186 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-5187        TCGA-BP-5189        TCGA-BP-5190        TCGA-BP-5191 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-5192        TCGA-BP-5194        TCGA-BP-5195        TCGA-BP-5196 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-5198        TCGA-BP-5199        TCGA-BP-5200        TCGA-BP-5201 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-5202        TCGA-CJ-4869        TCGA-CJ-4882        TCGA-CJ-4897 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-4901        TCGA-CJ-4902        TCGA-CJ-4903        TCGA-CJ-4904 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-4905        TCGA-CJ-4907        TCGA-CJ-4908        TCGA-CJ-4912 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-4913        TCGA-CJ-4916        TCGA-CJ-4918        TCGA-CJ-4920 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-4923        TCGA-CJ-5671        TCGA-CJ-5672        TCGA-CJ-5675 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-5676        TCGA-CJ-5677        TCGA-CJ-5678        TCGA-CJ-5679 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-5680        TCGA-CJ-5681        TCGA-CJ-5682        TCGA-CJ-5683 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-5684        TCGA-CJ-5686        TCGA-CJ-5689        TCGA-CJ-6027 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-6028        TCGA-CJ-6030        TCGA-CJ-6031        TCGA-CJ-6032 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-6033        TCGA-CW-5580        TCGA-CW-5581        TCGA-CW-5583 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CW-5584        TCGA-CW-5585        TCGA-CW-5587        TCGA-CW-5588 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CW-5589        TCGA-CW-5591        TCGA-CW-6087        TCGA-CW-6088 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CW-6090        TCGA-CW-6093        TCGA-CW-6097        TCGA-CZ-4853 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-4856        TCGA-CZ-4859        TCGA-CZ-4863        TCGA-CZ-4864 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-4865        TCGA-CZ-4866        TCGA-CZ-5451        TCGA-CZ-5452 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5453        TCGA-CZ-5454        TCGA-CZ-5455        TCGA-CZ-5456 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5457        TCGA-CZ-5458        TCGA-CZ-5459        TCGA-CZ-5460 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5461        TCGA-CZ-5462        TCGA-CZ-5463        TCGA-CZ-5464 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5465        TCGA-CZ-5466        TCGA-CZ-5467        TCGA-CZ-5468 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5469        TCGA-CZ-5470        TCGA-CZ-5982        TCGA-CZ-5984 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5985        TCGA-CZ-5986        TCGA-CZ-5987        TCGA-CZ-5988 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5989        TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5567 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5573        TCGA-DV-5574 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DV-5575        TCGA-DV-5576        TCGA-DV-A4VX        TCGA-DV-A4VZ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DV-A4W0        TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5906 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EU-5907        TCGA-MM-A563        TCGA-MM-A564        TCGA-MW-A4EC 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
D1V5, multiclass
D1V6, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           0               186
  CLUS_2           1               151
  CLUS_3           3               106
D1V7, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           3               194
  CLUS_2           1               178
  CLUS_3           1                96
D1V8, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           1                68
  CLUS_2           2               212
  CLUS_3           2               188
D1V9, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           0               115
  CLUS_2           3               188
  CLUS_3           2               167
D1V10, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           0                35
  CLUS_2           2               158
  CLUS_3           3               277
D1V11, multiclass
[1] "Remove cluster labels:" "1P GAIN CNV"           
clus
      1P GAIN CNV 1P GAIN WILD-TYPE 
                1               212 
       TCGA-A3-3317        TCGA-A3-3358        TCGA-A3-3387        TCGA-AK-3440 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AK-3458        TCGA-AK-3465        TCGA-B0-4698        TCGA-B0-4700 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4706        TCGA-B0-4710        TCGA-B0-4712        TCGA-B0-4810 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4811        TCGA-B0-4815        TCGA-B0-4816        TCGA-B0-4818 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4821        TCGA-B0-4833        TCGA-B0-4834        TCGA-B0-4836 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4837        TCGA-B0-4852        TCGA-B0-5075        TCGA-B0-5080 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5084        TCGA-B0-5085        TCGA-B0-5088        TCGA-B0-5399 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5400        TCGA-B0-5402        TCGA-B0-5690        TCGA-B0-5691 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5692        TCGA-B0-5693        TCGA-B0-5694        TCGA-B0-5695 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5696        TCGA-B0-5697        TCGA-B0-5698        TCGA-B0-5699 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5701        TCGA-B0-5702        TCGA-B0-5703        TCGA-B0-5705 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5706        TCGA-B0-5709        TCGA-B0-5710        TCGA-B0-5711 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5712        TCGA-B0-5713        TCGA-B0-5812        TCGA-B2-5633 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B2-5635        TCGA-B2-5639        TCGA-B2-5641        TCGA-B4-5377 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B4-5378        TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B8-4146        TCGA-B8-4153        TCGA-B8-4621        TCGA-B8-5545 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B8-5546        TCGA-B8-5549        TCGA-B8-5550        TCGA-B8-5551 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B8-5552        TCGA-B8-5553        TCGA-BP-4173        TCGA-BP-4331 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4340        TCGA-BP-4759        TCGA-BP-4761        TCGA-BP-4770 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4771        TCGA-BP-4787        TCGA-BP-4789        TCGA-BP-4790 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4797        TCGA-BP-4804        TCGA-BP-4807        TCGA-BP-4959 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4960        TCGA-BP-4961        TCGA-BP-4965        TCGA-BP-4967 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4968        TCGA-BP-4969        TCGA-BP-4970        TCGA-BP-4971 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4973        TCGA-BP-4974        TCGA-BP-4975        TCGA-BP-4976 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4977        TCGA-BP-4981        TCGA-BP-4982        TCGA-BP-4985 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4986        TCGA-BP-4987        TCGA-BP-4988        TCGA-BP-4989 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4992        TCGA-BP-4994        TCGA-BP-4995        TCGA-BP-4998 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-5000        TCGA-BP-5001        TCGA-BP-5007        TCGA-BP-5008 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-5009        TCGA-CJ-4635        TCGA-CJ-4870        TCGA-CJ-4875 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-4876        TCGA-CJ-4878        TCGA-CJ-4881        TCGA-CJ-4887 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-4888        TCGA-CJ-4889        TCGA-CJ-4890        TCGA-CJ-4891 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-4895        TCGA-CJ-4899        TCGA-CJ-4900        TCGA-CJ-5671 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-5672        TCGA-CJ-5675        TCGA-CJ-5676        TCGA-CJ-5677 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-5678        TCGA-CJ-5679        TCGA-CJ-5680        TCGA-CJ-5681 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-5682        TCGA-CJ-5683        TCGA-CJ-5684        TCGA-CJ-5686 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-5689        TCGA-CJ-6027        TCGA-CJ-6028        TCGA-CJ-6030 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-6031        TCGA-CJ-6032        TCGA-CJ-6033        TCGA-CW-5580 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CW-5581        TCGA-CW-5583        TCGA-CW-5584        TCGA-CW-5585 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CW-5587        TCGA-CW-5588        TCGA-CW-5589        TCGA-CW-5591 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CW-6087        TCGA-CW-6088        TCGA-CW-6090        TCGA-CW-6093 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CW-6097        TCGA-CZ-4854        TCGA-CZ-4857        TCGA-CZ-4860 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-4863        TCGA-CZ-4864        TCGA-CZ-4865        TCGA-CZ-4866 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5451        TCGA-CZ-5452        TCGA-CZ-5453        TCGA-CZ-5454 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5455        TCGA-CZ-5456        TCGA-CZ-5457        TCGA-CZ-5458 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5459        TCGA-CZ-5460        TCGA-CZ-5461        TCGA-CZ-5462 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5463        TCGA-CZ-5464        TCGA-CZ-5465        TCGA-CZ-5466 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5467        TCGA-CZ-5468        TCGA-CZ-5469        TCGA-CZ-5470 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5982        TCGA-CZ-5984        TCGA-CZ-5985        TCGA-CZ-5986 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5987        TCGA-CZ-5988        TCGA-CZ-5989        TCGA-DV-5565 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DV-5566        TCGA-DV-5567        TCGA-DV-5568        TCGA-DV-5569 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DV-5573        TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
D1V12, multiclass
[1] "Remove cluster labels:" "1P GAIN CNV"           
clus
      1P GAIN CNV 1P GAIN WILD-TYPE 
                1               212 
       TCGA-A3-3317        TCGA-A3-3358        TCGA-A3-3387        TCGA-AK-3440 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AK-3458        TCGA-AK-3465        TCGA-B0-4698        TCGA-B0-4700 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4706        TCGA-B0-4710        TCGA-B0-4712        TCGA-B0-4810 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4811        TCGA-B0-4815        TCGA-B0-4816        TCGA-B0-4818 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4821        TCGA-B0-4833        TCGA-B0-4834        TCGA-B0-4836 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4837        TCGA-B0-4852        TCGA-B0-5075        TCGA-B0-5080 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5084        TCGA-B0-5085        TCGA-B0-5088        TCGA-B0-5399 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5400        TCGA-B0-5402        TCGA-B0-5690        TCGA-B0-5691 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5692        TCGA-B0-5693        TCGA-B0-5694        TCGA-B0-5695 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5696        TCGA-B0-5697        TCGA-B0-5698        TCGA-B0-5699 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5701        TCGA-B0-5702        TCGA-B0-5703        TCGA-B0-5705 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5706        TCGA-B0-5709        TCGA-B0-5710        TCGA-B0-5711 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5712        TCGA-B0-5713        TCGA-B0-5812        TCGA-B2-5633 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B2-5635        TCGA-B2-5639        TCGA-B2-5641        TCGA-B4-5377 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B4-5378        TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B8-4146        TCGA-B8-4153        TCGA-B8-4621        TCGA-B8-5545 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B8-5546        TCGA-B8-5549        TCGA-B8-5550        TCGA-B8-5551 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B8-5552        TCGA-B8-5553        TCGA-BP-4173        TCGA-BP-4331 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4340        TCGA-BP-4759        TCGA-BP-4761        TCGA-BP-4770 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4771        TCGA-BP-4787        TCGA-BP-4789        TCGA-BP-4790 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4797        TCGA-BP-4804        TCGA-BP-4807        TCGA-BP-4959 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4960        TCGA-BP-4961        TCGA-BP-4965        TCGA-BP-4967 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4968        TCGA-BP-4969        TCGA-BP-4970        TCGA-BP-4971 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4973        TCGA-BP-4974        TCGA-BP-4975        TCGA-BP-4976 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4977        TCGA-BP-4981        TCGA-BP-4982        TCGA-BP-4985 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4986        TCGA-BP-4987        TCGA-BP-4988        TCGA-BP-4989 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4992        TCGA-BP-4994        TCGA-BP-4995        TCGA-BP-4998 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-5000        TCGA-BP-5001        TCGA-BP-5007        TCGA-BP-5008 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-5009        TCGA-CJ-4635        TCGA-CJ-4870        TCGA-CJ-4875 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-4876        TCGA-CJ-4878        TCGA-CJ-4881        TCGA-CJ-4887 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-4888        TCGA-CJ-4889        TCGA-CJ-4890        TCGA-CJ-4891 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-4895        TCGA-CJ-4899        TCGA-CJ-4900        TCGA-CJ-5671 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-5672        TCGA-CJ-5675        TCGA-CJ-5676        TCGA-CJ-5677 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-5678        TCGA-CJ-5679        TCGA-CJ-5680        TCGA-CJ-5681 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-5682        TCGA-CJ-5683        TCGA-CJ-5684        TCGA-CJ-5686 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-5689        TCGA-CJ-6027        TCGA-CJ-6028        TCGA-CJ-6030 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-6031        TCGA-CJ-6032        TCGA-CJ-6033        TCGA-CW-5580 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CW-5581        TCGA-CW-5583        TCGA-CW-5584        TCGA-CW-5585 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CW-5587        TCGA-CW-5588        TCGA-CW-5589        TCGA-CW-5591 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CW-6087        TCGA-CW-6088        TCGA-CW-6090        TCGA-CW-6093 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CW-6097        TCGA-CZ-4854        TCGA-CZ-4857        TCGA-CZ-4860 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-4863        TCGA-CZ-4864        TCGA-CZ-4865        TCGA-CZ-4866 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5451        TCGA-CZ-5452        TCGA-CZ-5453        TCGA-CZ-5454 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5455        TCGA-CZ-5456        TCGA-CZ-5457        TCGA-CZ-5458 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5459        TCGA-CZ-5460        TCGA-CZ-5461        TCGA-CZ-5462 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5463        TCGA-CZ-5464        TCGA-CZ-5465        TCGA-CZ-5466 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5467        TCGA-CZ-5468        TCGA-CZ-5469        TCGA-CZ-5470 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5982        TCGA-CZ-5984        TCGA-CZ-5985        TCGA-CZ-5986 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5987        TCGA-CZ-5988        TCGA-CZ-5989        TCGA-DV-5565 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DV-5566        TCGA-DV-5567        TCGA-DV-5568        TCGA-DV-5569 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DV-5573        TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 

Clustering(2) Variable = 1q gain
D2V1, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           3                30
  CLUS_2           4                20
  CLUS_3           1                12
D2V2, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           1                13
  CLUS_2           3                29
  CLUS_3           4                20
D2V3, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          26               138
  CLUS_2           5               211
  CLUS_3           1               123
D2V4, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           7                92
  CLUS_2           5               114
  CLUS_3           4                67
D2V5, multiclass
D2V6, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           8               178
  CLUS_2          14               138
  CLUS_3           6               103
D2V7, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          12               185
  CLUS_2          18               161
  CLUS_3           1                96
D2V8, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           1                68
  CLUS_2          15               199
  CLUS_3          15               175
D2V9, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           2               113
  CLUS_2          11               180
  CLUS_3          17               152
D2V10, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           0                35
  CLUS_2          13               147
  CLUS_3          17               263
D2V11, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           1                49
  CLUS_2           4                85
  CLUS_3           6                68
D2V12, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           5                52
  CLUS_2           4                88
  CLUS_3           2                62

Clustering(3) Variable = 2p gain
D3V1, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           4                29
  CLUS_2           2                22
  CLUS_3           0                13
D3V2, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           0                14
  CLUS_2           4                28
  CLUS_3           2                22
D3V3, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1          31               133
  CLUS_2          12               204
  CLUS_3           6               118
D3V4, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1          11                88
  CLUS_2           9               110
  CLUS_3           5                66
D3V5, multiclass
D3V6, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1          16               170
  CLUS_2          14               138
  CLUS_3          12                97
D3V7, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1          24               173
  CLUS_2          16               163
  CLUS_3           5                92
D3V8, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           2                67
  CLUS_2          25               189
  CLUS_3          18               172
D3V9, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           7               108
  CLUS_2          23               168
  CLUS_3          18               151
D3V10, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           1                34
  CLUS_2          13               147
  CLUS_3          34               246
D3V11, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           5                45
  CLUS_2           5                84
  CLUS_3          10                64
D3V12, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           4                53
  CLUS_2           8                84
  CLUS_3           8                56

Clustering(4) Variable = 2q gain
D4V1, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           4                29
  CLUS_2           2                22
  CLUS_3           0                13
D4V2, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           0                14
  CLUS_2           4                28
  CLUS_3           2                22
D4V3, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1          29               135
  CLUS_2          15               201
  CLUS_3           6               118
D4V4, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1          11                88
  CLUS_2          10               109
  CLUS_3           4                67
D4V5, multiclass
D4V6, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1          17               169
  CLUS_2          15               137
  CLUS_3          12                97
D4V7, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1          27               170
  CLUS_2          15               164
  CLUS_3           5                92
D4V8, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           2                67
  CLUS_2          27               187
  CLUS_3          18               172
D4V9, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           7               108
  CLUS_2          25               166
  CLUS_3          16               153
D4V10, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           1                34
  CLUS_2          13               147
  CLUS_3          34               246
D4V11, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           5                45
  CLUS_2           6                83
  CLUS_3           9                65
D4V12, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           3                54
  CLUS_2           9                83
  CLUS_3           8                56

Clustering(5) Variable = 3p gain
D5V1, multiclass
[1] "Remove cluster labels:" "3P GAIN CNV"           
clus
      3P GAIN CNV 3P GAIN WILD-TYPE 
                2                68 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3455        TCGA-AK-3456 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778        TCGA-B2-3923 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099        TCGA-B2-4102 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151        TCGA-B8-4154 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161        TCGA-BP-4162 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167        TCGA-CJ-4634 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638        TCGA-CJ-4639 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643        TCGA-CJ-4644 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D5V2, multiclass
[1] "Remove cluster labels:" "3P GAIN CNV"           
clus
      3P GAIN CNV 3P GAIN WILD-TYPE 
                2                68 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3455        TCGA-AK-3456 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778        TCGA-B2-3923 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099        TCGA-B2-4102 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151        TCGA-B8-4154 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161        TCGA-BP-4162 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167        TCGA-CJ-4634 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638        TCGA-CJ-4639 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643        TCGA-CJ-4644 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D5V3, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           4               160
  CLUS_2           1               215
  CLUS_3           2               122
D5V4, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           1                98
  CLUS_2           1               118
  CLUS_3           1                70
D5V5, multiclass
D5V6, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           0               186
  CLUS_2           1               151
  CLUS_3           5               104
D5V7, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           1               196
  CLUS_2           4               175
  CLUS_3           2                95
D5V8, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           2                67
  CLUS_2           1               213
  CLUS_3           4               186
D5V9, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           1               114
  CLUS_2           0               191
  CLUS_3           6               163
D5V10, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           2                33
  CLUS_2           3               157
  CLUS_3           2               278
D5V11, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           1                49
  CLUS_2           0                89
  CLUS_3           2                72
D5V12, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           0                57
  CLUS_2           1                91
  CLUS_3           2                62

Clustering(6) Variable = 3q gain
D6V1, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           0                33
  CLUS_2           4                20
  CLUS_3           1                12
D6V2, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           1                13
  CLUS_2           0                32
  CLUS_3           4                20
D6V3, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1          23               141
  CLUS_2           3               213
  CLUS_3           3               121
D6V4, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1          10                89
  CLUS_2           3               116
  CLUS_3           3                68
D6V5, multiclass
D6V6, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           3               183
  CLUS_2           8               144
  CLUS_3          15                94
D6V7, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           4               193
  CLUS_2          20               159
  CLUS_3           4                93
D6V8, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           5                64
  CLUS_2           5               209
  CLUS_3          18               172
D6V9, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           5               110
  CLUS_2           3               188
  CLUS_3          20               149
D6V10, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           5                30
  CLUS_2          14               146
  CLUS_3           9               271
D6V11, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           2                48
  CLUS_2           1                88
  CLUS_3          11                63
D6V12, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           5                52
  CLUS_2           3                89
  CLUS_3           6                58

Clustering(7) Variable = 4p gain
D7V1, multiclass
[1] "Remove cluster labels:" "4P GAIN CNV"           
clus
      4P GAIN CNV 4P GAIN WILD-TYPE 
                1                69 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-4644 
"4P GAIN WILD-TYPE" 
D7V2, multiclass
[1] "Remove cluster labels:" "4P GAIN CNV"           
clus
      4P GAIN CNV 4P GAIN WILD-TYPE 
                1                69 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-4644 
"4P GAIN WILD-TYPE" 
D7V3, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           5               159
  CLUS_2           1               215
  CLUS_3           2               122
D7V4, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           2                97
  CLUS_2           1               118
  CLUS_3           0                71
D7V5, multiclass
D7V6, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           1               185
  CLUS_2           1               151
  CLUS_3           4               105
D7V7, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           0               197
  CLUS_2           4               175
  CLUS_3           3                94
D7V8, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           2                67
  CLUS_2           2               212
  CLUS_3           3               187
D7V9, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           0               115
  CLUS_2           0               191
  CLUS_3           8               161
D7V10, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           2                33
  CLUS_2           4               156
  CLUS_3           2               278
D7V11, multiclass
[1] "Remove cluster labels:" "4P GAIN CNV"           
clus
      4P GAIN CNV 4P GAIN WILD-TYPE 
                2               211 
       TCGA-A3-3317        TCGA-A3-3358        TCGA-A3-3387        TCGA-AK-3440 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AK-3458        TCGA-AK-3465        TCGA-B0-4698        TCGA-B0-4700 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B0-4706        TCGA-B0-4710        TCGA-B0-4712        TCGA-B0-4810 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B0-4811        TCGA-B0-4815        TCGA-B0-4816        TCGA-B0-4818 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B0-4821        TCGA-B0-4833        TCGA-B0-4834        TCGA-B0-4836 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B0-4837        TCGA-B0-4852        TCGA-B0-5075        TCGA-B0-5080 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B0-5084        TCGA-B0-5085        TCGA-B0-5088        TCGA-B0-5399 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B0-5400        TCGA-B0-5402        TCGA-B0-5690        TCGA-B0-5691 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B0-5692        TCGA-B0-5693        TCGA-B0-5694        TCGA-B0-5695 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B0-5696        TCGA-B0-5697        TCGA-B0-5698        TCGA-B0-5699 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B0-5701        TCGA-B0-5702        TCGA-B0-5703        TCGA-B0-5705 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B0-5706        TCGA-B0-5709        TCGA-B0-5710        TCGA-B0-5711 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B0-5712        TCGA-B0-5713        TCGA-B0-5812        TCGA-B2-5633 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B2-5635        TCGA-B2-5639        TCGA-B2-5641        TCGA-B4-5377 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B4-5378        TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B8-4146        TCGA-B8-4153        TCGA-B8-4621        TCGA-B8-5545 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B8-5546        TCGA-B8-5549        TCGA-B8-5550        TCGA-B8-5551 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B8-5552        TCGA-B8-5553        TCGA-BP-4173        TCGA-BP-4331 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BP-4340        TCGA-BP-4759        TCGA-BP-4761        TCGA-BP-4770 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BP-4771        TCGA-BP-4787        TCGA-BP-4789        TCGA-BP-4790 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BP-4797        TCGA-BP-4804        TCGA-BP-4807        TCGA-BP-4959 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BP-4960        TCGA-BP-4961        TCGA-BP-4965        TCGA-BP-4967 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BP-4968        TCGA-BP-4969        TCGA-BP-4970        TCGA-BP-4971 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BP-4973        TCGA-BP-4974        TCGA-BP-4975        TCGA-BP-4976 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BP-4981        TCGA-BP-4982        TCGA-BP-4985        TCGA-BP-4986 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BP-4987        TCGA-BP-4988        TCGA-BP-4992        TCGA-BP-4994 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BP-4995        TCGA-BP-4998        TCGA-BP-5000        TCGA-BP-5001 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BP-5007        TCGA-BP-5008        TCGA-BP-5009        TCGA-CJ-4635 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-4870        TCGA-CJ-4875        TCGA-CJ-4876        TCGA-CJ-4878 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-4881        TCGA-CJ-4887        TCGA-CJ-4888        TCGA-CJ-4889 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-4890        TCGA-CJ-4891        TCGA-CJ-4895        TCGA-CJ-4899 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-4900        TCGA-CJ-5671        TCGA-CJ-5672        TCGA-CJ-5675 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-5676        TCGA-CJ-5677        TCGA-CJ-5678        TCGA-CJ-5679 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-5680        TCGA-CJ-5681        TCGA-CJ-5682        TCGA-CJ-5683 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-5684        TCGA-CJ-5686        TCGA-CJ-5689        TCGA-CJ-6027 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-6028        TCGA-CJ-6030        TCGA-CJ-6031        TCGA-CJ-6032 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-6033        TCGA-CW-5580        TCGA-CW-5581        TCGA-CW-5583 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CW-5584        TCGA-CW-5585        TCGA-CW-5587        TCGA-CW-5588 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CW-5589        TCGA-CW-5591        TCGA-CW-6087        TCGA-CW-6088 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CW-6090        TCGA-CW-6093        TCGA-CW-6097        TCGA-CZ-4854 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-4857        TCGA-CZ-4858        TCGA-CZ-4860        TCGA-CZ-4863 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-4864        TCGA-CZ-4865        TCGA-CZ-4866        TCGA-CZ-5451 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-5452        TCGA-CZ-5453        TCGA-CZ-5454        TCGA-CZ-5455 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-5456        TCGA-CZ-5457        TCGA-CZ-5458        TCGA-CZ-5459 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-5460        TCGA-CZ-5461        TCGA-CZ-5462        TCGA-CZ-5463 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-5464        TCGA-CZ-5465        TCGA-CZ-5466        TCGA-CZ-5467 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-5468        TCGA-CZ-5469        TCGA-CZ-5470        TCGA-CZ-5982 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-5984        TCGA-CZ-5985        TCGA-CZ-5986        TCGA-CZ-5987 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-5988        TCGA-CZ-5989        TCGA-DV-5565        TCGA-DV-5566 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DV-5567        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5573 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576        TCGA-EU-5904 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V12, multiclass
[1] "Remove cluster labels:" "4P GAIN CNV"           
clus
      4P GAIN CNV 4P GAIN WILD-TYPE 
                2               211 
       TCGA-A3-3317        TCGA-A3-3358        TCGA-A3-3387        TCGA-AK-3440 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AK-3458        TCGA-AK-3465        TCGA-B0-4698        TCGA-B0-4700 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B0-4706        TCGA-B0-4710        TCGA-B0-4712        TCGA-B0-4810 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B0-4811        TCGA-B0-4815        TCGA-B0-4816        TCGA-B0-4818 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B0-4821        TCGA-B0-4833        TCGA-B0-4834        TCGA-B0-4836 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B0-4837        TCGA-B0-4852        TCGA-B0-5075        TCGA-B0-5080 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B0-5084        TCGA-B0-5085        TCGA-B0-5088        TCGA-B0-5399 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B0-5400        TCGA-B0-5402        TCGA-B0-5690        TCGA-B0-5691 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B0-5692        TCGA-B0-5693        TCGA-B0-5694        TCGA-B0-5695 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B0-5696        TCGA-B0-5697        TCGA-B0-5698        TCGA-B0-5699 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B0-5701        TCGA-B0-5702        TCGA-B0-5703        TCGA-B0-5705 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B0-5706        TCGA-B0-5709        TCGA-B0-5710        TCGA-B0-5711 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B0-5712        TCGA-B0-5713        TCGA-B0-5812        TCGA-B2-5633 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B2-5635        TCGA-B2-5639        TCGA-B2-5641        TCGA-B4-5377 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B4-5378        TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B8-4146        TCGA-B8-4153        TCGA-B8-4621        TCGA-B8-5545 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B8-5546        TCGA-B8-5549        TCGA-B8-5550        TCGA-B8-5551 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B8-5552        TCGA-B8-5553        TCGA-BP-4173        TCGA-BP-4331 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BP-4340        TCGA-BP-4759        TCGA-BP-4761        TCGA-BP-4770 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BP-4771        TCGA-BP-4787        TCGA-BP-4789        TCGA-BP-4790 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BP-4797        TCGA-BP-4804        TCGA-BP-4807        TCGA-BP-4959 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BP-4960        TCGA-BP-4961        TCGA-BP-4965        TCGA-BP-4967 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BP-4968        TCGA-BP-4969        TCGA-BP-4970        TCGA-BP-4971 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BP-4973        TCGA-BP-4974        TCGA-BP-4975        TCGA-BP-4976 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BP-4981        TCGA-BP-4982        TCGA-BP-4985        TCGA-BP-4986 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BP-4987        TCGA-BP-4988        TCGA-BP-4992        TCGA-BP-4994 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BP-4995        TCGA-BP-4998        TCGA-BP-5000        TCGA-BP-5001 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BP-5007        TCGA-BP-5008        TCGA-BP-5009        TCGA-CJ-4635 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-4870        TCGA-CJ-4875        TCGA-CJ-4876        TCGA-CJ-4878 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-4881        TCGA-CJ-4887        TCGA-CJ-4888        TCGA-CJ-4889 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-4890        TCGA-CJ-4891        TCGA-CJ-4895        TCGA-CJ-4899 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-4900        TCGA-CJ-5671        TCGA-CJ-5672        TCGA-CJ-5675 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-5676        TCGA-CJ-5677        TCGA-CJ-5678        TCGA-CJ-5679 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-5680        TCGA-CJ-5681        TCGA-CJ-5682        TCGA-CJ-5683 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-5684        TCGA-CJ-5686        TCGA-CJ-5689        TCGA-CJ-6027 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-6028        TCGA-CJ-6030        TCGA-CJ-6031        TCGA-CJ-6032 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-6033        TCGA-CW-5580        TCGA-CW-5581        TCGA-CW-5583 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CW-5584        TCGA-CW-5585        TCGA-CW-5587        TCGA-CW-5588 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CW-5589        TCGA-CW-5591        TCGA-CW-6087        TCGA-CW-6088 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CW-6090        TCGA-CW-6093        TCGA-CW-6097        TCGA-CZ-4854 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-4857        TCGA-CZ-4858        TCGA-CZ-4860        TCGA-CZ-4863 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-4864        TCGA-CZ-4865        TCGA-CZ-4866        TCGA-CZ-5451 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-5452        TCGA-CZ-5453        TCGA-CZ-5454        TCGA-CZ-5455 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-5456        TCGA-CZ-5457        TCGA-CZ-5458        TCGA-CZ-5459 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-5460        TCGA-CZ-5461        TCGA-CZ-5462        TCGA-CZ-5463 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-5464        TCGA-CZ-5465        TCGA-CZ-5466        TCGA-CZ-5467 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-5468        TCGA-CZ-5469        TCGA-CZ-5470        TCGA-CZ-5982 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-5984        TCGA-CZ-5985        TCGA-CZ-5986        TCGA-CZ-5987 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-5988        TCGA-CZ-5989        TCGA-DV-5565        TCGA-DV-5566 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DV-5567        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5573 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576        TCGA-EU-5904 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 

Clustering(8) Variable = 4q gain
D8V1, multiclass
[1] "Remove cluster labels:" "4Q GAIN CNV"           
clus
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                1                69 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-4644 
"4Q GAIN WILD-TYPE" 
D8V2, multiclass
[1] "Remove cluster labels:" "4Q GAIN CNV"           
clus
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                1                69 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-4644 
"4Q GAIN WILD-TYPE" 
D8V3, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           4               160
  CLUS_2           2               214
  CLUS_3           2               122
D8V4, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           1                98
  CLUS_2           2               117
  CLUS_3           0                71
D8V5, multiclass
D8V6, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           2               184
  CLUS_2           1               151
  CLUS_3           3               106
D8V7, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           0               197
  CLUS_2           3               176
  CLUS_3           4                93
D8V8, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           2                67
  CLUS_2           3               211
  CLUS_3           2               188
D8V9, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           1               114
  CLUS_2           0               191
  CLUS_3           7               162
D8V10, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           2                33
  CLUS_2           3               157
  CLUS_3           3               277
D8V11, multiclass
[1] "Remove cluster labels:" "4Q GAIN CNV"           
clus
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                2               211 
       TCGA-A3-3317        TCGA-A3-3358        TCGA-A3-3387        TCGA-AK-3440 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AK-3458        TCGA-AK-3465        TCGA-B0-4698        TCGA-B0-4700 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B0-4706        TCGA-B0-4710        TCGA-B0-4712        TCGA-B0-4810 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B0-4811        TCGA-B0-4815        TCGA-B0-4816        TCGA-B0-4818 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B0-4821        TCGA-B0-4833        TCGA-B0-4834        TCGA-B0-4836 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B0-4837        TCGA-B0-4852        TCGA-B0-5075        TCGA-B0-5080 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B0-5084        TCGA-B0-5085        TCGA-B0-5088        TCGA-B0-5399 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B0-5400        TCGA-B0-5402        TCGA-B0-5690        TCGA-B0-5691 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B0-5692        TCGA-B0-5693        TCGA-B0-5694        TCGA-B0-5695 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B0-5696        TCGA-B0-5697        TCGA-B0-5698        TCGA-B0-5699 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B0-5701        TCGA-B0-5702        TCGA-B0-5703        TCGA-B0-5705 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B0-5706        TCGA-B0-5709        TCGA-B0-5710        TCGA-B0-5711 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B0-5712        TCGA-B0-5713        TCGA-B0-5812        TCGA-B2-5633 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B2-5635        TCGA-B2-5639        TCGA-B2-5641        TCGA-B4-5377 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B4-5378        TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B8-4146        TCGA-B8-4153        TCGA-B8-4621        TCGA-B8-5545 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B8-5546        TCGA-B8-5549        TCGA-B8-5550        TCGA-B8-5551 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B8-5552        TCGA-B8-5553        TCGA-BP-4173        TCGA-BP-4331 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BP-4340        TCGA-BP-4759        TCGA-BP-4761        TCGA-BP-4770 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BP-4771        TCGA-BP-4787        TCGA-BP-4789        TCGA-BP-4790 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BP-4797        TCGA-BP-4804        TCGA-BP-4807        TCGA-BP-4959 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BP-4960        TCGA-BP-4961        TCGA-BP-4965        TCGA-BP-4967 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BP-4968        TCGA-BP-4969        TCGA-BP-4970        TCGA-BP-4971 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BP-4973        TCGA-BP-4974        TCGA-BP-4975        TCGA-BP-4976 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BP-4981        TCGA-BP-4982        TCGA-BP-4985        TCGA-BP-4986 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BP-4987        TCGA-BP-4988        TCGA-BP-4992        TCGA-BP-4994 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BP-4995        TCGA-BP-4998        TCGA-BP-5000        TCGA-BP-5001 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BP-5007        TCGA-BP-5008        TCGA-BP-5009        TCGA-CJ-4635 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-4870        TCGA-CJ-4875        TCGA-CJ-4876        TCGA-CJ-4878 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-4881        TCGA-CJ-4887        TCGA-CJ-4888        TCGA-CJ-4889 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-4890        TCGA-CJ-4891        TCGA-CJ-4895        TCGA-CJ-4899 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-4900        TCGA-CJ-5671        TCGA-CJ-5672        TCGA-CJ-5675 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-5676        TCGA-CJ-5677        TCGA-CJ-5678        TCGA-CJ-5679 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-5680        TCGA-CJ-5681        TCGA-CJ-5682        TCGA-CJ-5683 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-5684        TCGA-CJ-5686        TCGA-CJ-5689        TCGA-CJ-6027 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-6028        TCGA-CJ-6030        TCGA-CJ-6031        TCGA-CJ-6032 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-6033        TCGA-CW-5580        TCGA-CW-5581        TCGA-CW-5583 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CW-5584        TCGA-CW-5585        TCGA-CW-5587        TCGA-CW-5588 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CW-5589        TCGA-CW-5591        TCGA-CW-6087        TCGA-CW-6088 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CW-6090        TCGA-CW-6093        TCGA-CW-6097        TCGA-CZ-4854 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-4857        TCGA-CZ-4858        TCGA-CZ-4860        TCGA-CZ-4863 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-4864        TCGA-CZ-4865        TCGA-CZ-4866        TCGA-CZ-5451 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-5452        TCGA-CZ-5453        TCGA-CZ-5454        TCGA-CZ-5455 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-5456        TCGA-CZ-5457        TCGA-CZ-5458        TCGA-CZ-5459 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-5460        TCGA-CZ-5461        TCGA-CZ-5462        TCGA-CZ-5463 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-5464        TCGA-CZ-5465        TCGA-CZ-5466        TCGA-CZ-5467 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-5468        TCGA-CZ-5469        TCGA-CZ-5470        TCGA-CZ-5982 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-5984        TCGA-CZ-5985        TCGA-CZ-5986        TCGA-CZ-5987 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-5988        TCGA-CZ-5989        TCGA-DV-5565        TCGA-DV-5566 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DV-5567        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5573 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576        TCGA-EU-5904 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V12, multiclass
[1] "Remove cluster labels:" "4Q GAIN CNV"           
clus
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                2               211 
       TCGA-A3-3317        TCGA-A3-3358        TCGA-A3-3387        TCGA-AK-3440 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AK-3458        TCGA-AK-3465        TCGA-B0-4698        TCGA-B0-4700 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B0-4706        TCGA-B0-4710        TCGA-B0-4712        TCGA-B0-4810 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B0-4811        TCGA-B0-4815        TCGA-B0-4816        TCGA-B0-4818 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B0-4821        TCGA-B0-4833        TCGA-B0-4834        TCGA-B0-4836 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B0-4837        TCGA-B0-4852        TCGA-B0-5075        TCGA-B0-5080 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B0-5084        TCGA-B0-5085        TCGA-B0-5088        TCGA-B0-5399 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B0-5400        TCGA-B0-5402        TCGA-B0-5690        TCGA-B0-5691 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B0-5692        TCGA-B0-5693        TCGA-B0-5694        TCGA-B0-5695 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B0-5696        TCGA-B0-5697        TCGA-B0-5698        TCGA-B0-5699 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B0-5701        TCGA-B0-5702        TCGA-B0-5703        TCGA-B0-5705 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B0-5706        TCGA-B0-5709        TCGA-B0-5710        TCGA-B0-5711 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B0-5712        TCGA-B0-5713        TCGA-B0-5812        TCGA-B2-5633 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B2-5635        TCGA-B2-5639        TCGA-B2-5641        TCGA-B4-5377 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B4-5378        TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B8-4146        TCGA-B8-4153        TCGA-B8-4621        TCGA-B8-5545 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B8-5546        TCGA-B8-5549        TCGA-B8-5550        TCGA-B8-5551 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B8-5552        TCGA-B8-5553        TCGA-BP-4173        TCGA-BP-4331 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BP-4340        TCGA-BP-4759        TCGA-BP-4761        TCGA-BP-4770 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BP-4771        TCGA-BP-4787        TCGA-BP-4789        TCGA-BP-4790 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BP-4797        TCGA-BP-4804        TCGA-BP-4807        TCGA-BP-4959 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BP-4960        TCGA-BP-4961        TCGA-BP-4965        TCGA-BP-4967 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BP-4968        TCGA-BP-4969        TCGA-BP-4970        TCGA-BP-4971 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BP-4973        TCGA-BP-4974        TCGA-BP-4975        TCGA-BP-4976 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BP-4981        TCGA-BP-4982        TCGA-BP-4985        TCGA-BP-4986 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BP-4987        TCGA-BP-4988        TCGA-BP-4992        TCGA-BP-4994 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BP-4995        TCGA-BP-4998        TCGA-BP-5000        TCGA-BP-5001 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BP-5007        TCGA-BP-5008        TCGA-BP-5009        TCGA-CJ-4635 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-4870        TCGA-CJ-4875        TCGA-CJ-4876        TCGA-CJ-4878 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-4881        TCGA-CJ-4887        TCGA-CJ-4888        TCGA-CJ-4889 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-4890        TCGA-CJ-4891        TCGA-CJ-4895        TCGA-CJ-4899 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-4900        TCGA-CJ-5671        TCGA-CJ-5672        TCGA-CJ-5675 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-5676        TCGA-CJ-5677        TCGA-CJ-5678        TCGA-CJ-5679 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-5680        TCGA-CJ-5681        TCGA-CJ-5682        TCGA-CJ-5683 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-5684        TCGA-CJ-5686        TCGA-CJ-5689        TCGA-CJ-6027 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-6028        TCGA-CJ-6030        TCGA-CJ-6031        TCGA-CJ-6032 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-6033        TCGA-CW-5580        TCGA-CW-5581        TCGA-CW-5583 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CW-5584        TCGA-CW-5585        TCGA-CW-5587        TCGA-CW-5588 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CW-5589        TCGA-CW-5591        TCGA-CW-6087        TCGA-CW-6088 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CW-6090        TCGA-CW-6093        TCGA-CW-6097        TCGA-CZ-4854 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-4857        TCGA-CZ-4858        TCGA-CZ-4860        TCGA-CZ-4863 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-4864        TCGA-CZ-4865        TCGA-CZ-4866        TCGA-CZ-5451 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-5452        TCGA-CZ-5453        TCGA-CZ-5454        TCGA-CZ-5455 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-5456        TCGA-CZ-5457        TCGA-CZ-5458        TCGA-CZ-5459 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-5460        TCGA-CZ-5461        TCGA-CZ-5462        TCGA-CZ-5463 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-5464        TCGA-CZ-5465        TCGA-CZ-5466        TCGA-CZ-5467 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-5468        TCGA-CZ-5469        TCGA-CZ-5470        TCGA-CZ-5982 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-5984        TCGA-CZ-5985        TCGA-CZ-5986        TCGA-CZ-5987 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-5988        TCGA-CZ-5989        TCGA-DV-5565        TCGA-DV-5566 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DV-5567        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5573 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576        TCGA-EU-5904 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 

Clustering(9) Variable = 5p gain
D9V1, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           9                24
  CLUS_2           4                20
  CLUS_3           2                11
D9V2, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           2                12
  CLUS_2           9                23
  CLUS_3           4                20
D9V3, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          64               100
  CLUS_2          57               159
  CLUS_3          22               102
D9V4, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          33                66
  CLUS_2          31                88
  CLUS_3          15                56
D9V5, multiclass
D9V6, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          44               142
  CLUS_2          54                98
  CLUS_3          30                79
D9V7, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          63               134
  CLUS_2          52               127
  CLUS_3          18                79
D9V8, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          10                59
  CLUS_2          71               143
  CLUS_3          52               138
D9V9, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          23                92
  CLUS_2          63               128
  CLUS_3          53               116
D9V10, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           3                32
  CLUS_2          44               116
  CLUS_3          92               188
D9V11, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           9                41
  CLUS_2          25                64
  CLUS_3          26                48
D9V12, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          22                35
  CLUS_2          27                65
  CLUS_3          11                53

Clustering(10) Variable = 5q gain
D10V1, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          13                20
  CLUS_2           4                20
  CLUS_3           2                11
D10V2, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           2                12
  CLUS_2          13                19
  CLUS_3           4                20
D10V3, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          65                99
  CLUS_2          68               148
  CLUS_3          26                98
D10V4, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          38                61
  CLUS_2          36                83
  CLUS_3          18                53
D10V5, multiclass
D10V6, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          53               133
  CLUS_2          57                95
  CLUS_3          32                77
D10V7, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          73               124
  CLUS_2          53               126
  CLUS_3          22                75
D10V8, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          12                57
  CLUS_2          80               134
  CLUS_3          56               134
D10V9, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          29                86
  CLUS_2          70               121
  CLUS_3          53               116
D10V10, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           3                32
  CLUS_2          47               113
  CLUS_3         102               178
D10V11, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          11                39
  CLUS_2          28                61
  CLUS_3          25                49
D10V12, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          22                35
  CLUS_2          30                62
  CLUS_3          12                52

Clustering(11) Variable = 6p gain
D11V1, multiclass
[1] "Remove cluster labels:" "6P GAIN CNV"           
clus
      6P GAIN CNV 6P GAIN WILD-TYPE 
                1                69 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319        TCGA-A3-3320 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324        TCGA-A3-3325 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335        TCGA-A3-3336 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347        TCGA-A3-3349 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359        TCGA-A3-3362 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372        TCGA-A3-3374 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-4644 
"6P GAIN WILD-TYPE" 
D11V2, multiclass
[1] "Remove cluster labels:" "6P GAIN CNV"           
clus
      6P GAIN CNV 6P GAIN WILD-TYPE 
                1                69 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319        TCGA-A3-3320 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324        TCGA-A3-3325 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335        TCGA-A3-3336 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347        TCGA-A3-3349 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359        TCGA-A3-3362 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372        TCGA-A3-3374 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-4644 
"6P GAIN WILD-TYPE" 
D11V3, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           2               162
  CLUS_2           2               214
  CLUS_3           2               122
D11V4, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           2                97
  CLUS_2           2               117
  CLUS_3           0                71
D11V5, multiclass
D11V6, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           2               184
  CLUS_2           2               150
  CLUS_3           2               107
D11V7, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           2               195
  CLUS_2           1               178
  CLUS_3           3                94
D11V8, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           1                68
  CLUS_2           4               210
  CLUS_3           1               189
D11V9, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           3               112
  CLUS_2           2               189
  CLUS_3           1               168
D11V10, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           1                34
  CLUS_2           1               159
  CLUS_3           4               276
D11V11, multiclass
[1] "Remove cluster labels:" "6P GAIN CNV"           
clus
      6P GAIN CNV 6P GAIN WILD-TYPE 
                2               211 
       TCGA-A3-3317        TCGA-A3-3358        TCGA-A3-3387        TCGA-AK-3440 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AK-3458        TCGA-AK-3465        TCGA-B0-4698        TCGA-B0-4700 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B0-4706        TCGA-B0-4710        TCGA-B0-4712        TCGA-B0-4810 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B0-4815        TCGA-B0-4816        TCGA-B0-4818        TCGA-B0-4821 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B0-4833        TCGA-B0-4834        TCGA-B0-4836        TCGA-B0-4837 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B0-4852        TCGA-B0-5075        TCGA-B0-5080        TCGA-B0-5084 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B0-5085        TCGA-B0-5088        TCGA-B0-5399        TCGA-B0-5400 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B0-5402        TCGA-B0-5690        TCGA-B0-5691        TCGA-B0-5692 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B0-5693        TCGA-B0-5694        TCGA-B0-5695        TCGA-B0-5696 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B0-5697        TCGA-B0-5698        TCGA-B0-5699        TCGA-B0-5701 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B0-5702        TCGA-B0-5703        TCGA-B0-5705        TCGA-B0-5706 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B0-5709        TCGA-B0-5710        TCGA-B0-5711        TCGA-B0-5712 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B0-5713        TCGA-B0-5812        TCGA-B2-5633        TCGA-B2-5635 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B2-5639        TCGA-B2-5641        TCGA-B4-5377        TCGA-B4-5378 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835        TCGA-B4-5836 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844        TCGA-B8-4146 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B8-4153        TCGA-B8-4621        TCGA-B8-5545        TCGA-B8-5546 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B8-5549        TCGA-B8-5550        TCGA-B8-5551        TCGA-B8-5552 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B8-5553        TCGA-BP-4173        TCGA-BP-4331        TCGA-BP-4340 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BP-4759        TCGA-BP-4761        TCGA-BP-4770        TCGA-BP-4771 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BP-4787        TCGA-BP-4789        TCGA-BP-4790        TCGA-BP-4797 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BP-4804        TCGA-BP-4807        TCGA-BP-4959        TCGA-BP-4960 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BP-4961        TCGA-BP-4965        TCGA-BP-4967        TCGA-BP-4968 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BP-4969        TCGA-BP-4970        TCGA-BP-4971        TCGA-BP-4973 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BP-4974        TCGA-BP-4975        TCGA-BP-4976        TCGA-BP-4977 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BP-4981        TCGA-BP-4982        TCGA-BP-4985        TCGA-BP-4986 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BP-4987        TCGA-BP-4988        TCGA-BP-4989        TCGA-BP-4992 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BP-4994        TCGA-BP-4995        TCGA-BP-4998        TCGA-BP-5000 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BP-5001        TCGA-BP-5007        TCGA-BP-5008        TCGA-BP-5009 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-4635        TCGA-CJ-4870        TCGA-CJ-4875        TCGA-CJ-4876 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-4878        TCGA-CJ-4881        TCGA-CJ-4887        TCGA-CJ-4888 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-4889        TCGA-CJ-4890        TCGA-CJ-4891        TCGA-CJ-4895 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-4899        TCGA-CJ-4900        TCGA-CJ-5671        TCGA-CJ-5672 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-5675        TCGA-CJ-5676        TCGA-CJ-5677        TCGA-CJ-5678 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-5679        TCGA-CJ-5680        TCGA-CJ-5681        TCGA-CJ-5682 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-5683        TCGA-CJ-5684        TCGA-CJ-5686        TCGA-CJ-5689 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-6027        TCGA-CJ-6028        TCGA-CJ-6030        TCGA-CJ-6031 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-6032        TCGA-CJ-6033        TCGA-CW-5580        TCGA-CW-5581 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CW-5583        TCGA-CW-5584        TCGA-CW-5585        TCGA-CW-5587 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CW-5588        TCGA-CW-5589        TCGA-CW-5591        TCGA-CW-6087 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CW-6088        TCGA-CW-6090        TCGA-CW-6093        TCGA-CW-6097 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CZ-4854        TCGA-CZ-4857        TCGA-CZ-4858        TCGA-CZ-4860 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CZ-4863        TCGA-CZ-4864        TCGA-CZ-4865        TCGA-CZ-4866 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CZ-5451        TCGA-CZ-5452        TCGA-CZ-5453        TCGA-CZ-5454 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CZ-5455        TCGA-CZ-5456        TCGA-CZ-5457        TCGA-CZ-5458 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CZ-5459        TCGA-CZ-5460        TCGA-CZ-5461        TCGA-CZ-5462 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CZ-5463        TCGA-CZ-5464        TCGA-CZ-5465        TCGA-CZ-5466 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CZ-5467        TCGA-CZ-5468        TCGA-CZ-5470        TCGA-CZ-5982 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CZ-5984        TCGA-CZ-5985        TCGA-CZ-5986        TCGA-CZ-5987 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CZ-5988        TCGA-CZ-5989        TCGA-DV-5565        TCGA-DV-5566 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DV-5567        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5573 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576        TCGA-EU-5904 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
D11V12, multiclass
[1] "Remove cluster labels:" "6P GAIN CNV"           
clus
      6P GAIN CNV 6P GAIN WILD-TYPE 
                2               211 
       TCGA-A3-3317        TCGA-A3-3358        TCGA-A3-3387        TCGA-AK-3440 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AK-3458        TCGA-AK-3465        TCGA-B0-4698        TCGA-B0-4700 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B0-4706        TCGA-B0-4710        TCGA-B0-4712        TCGA-B0-4810 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B0-4815        TCGA-B0-4816        TCGA-B0-4818        TCGA-B0-4821 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B0-4833        TCGA-B0-4834        TCGA-B0-4836        TCGA-B0-4837 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B0-4852        TCGA-B0-5075        TCGA-B0-5080        TCGA-B0-5084 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B0-5085        TCGA-B0-5088        TCGA-B0-5399        TCGA-B0-5400 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B0-5402        TCGA-B0-5690        TCGA-B0-5691        TCGA-B0-5692 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B0-5693        TCGA-B0-5694        TCGA-B0-5695        TCGA-B0-5696 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B0-5697        TCGA-B0-5698        TCGA-B0-5699        TCGA-B0-5701 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B0-5702        TCGA-B0-5703        TCGA-B0-5705        TCGA-B0-5706 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B0-5709        TCGA-B0-5710        TCGA-B0-5711        TCGA-B0-5712 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B0-5713        TCGA-B0-5812        TCGA-B2-5633        TCGA-B2-5635 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B2-5639        TCGA-B2-5641        TCGA-B4-5377        TCGA-B4-5378 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835        TCGA-B4-5836 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844        TCGA-B8-4146 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B8-4153        TCGA-B8-4621        TCGA-B8-5545        TCGA-B8-5546 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B8-5549        TCGA-B8-5550        TCGA-B8-5551        TCGA-B8-5552 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B8-5553        TCGA-BP-4173        TCGA-BP-4331        TCGA-BP-4340 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BP-4759        TCGA-BP-4761        TCGA-BP-4770        TCGA-BP-4771 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BP-4787        TCGA-BP-4789        TCGA-BP-4790        TCGA-BP-4797 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BP-4804        TCGA-BP-4807        TCGA-BP-4959        TCGA-BP-4960 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BP-4961        TCGA-BP-4965        TCGA-BP-4967        TCGA-BP-4968 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BP-4969        TCGA-BP-4970        TCGA-BP-4971        TCGA-BP-4973 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BP-4974        TCGA-BP-4975        TCGA-BP-4976        TCGA-BP-4977 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BP-4981        TCGA-BP-4982        TCGA-BP-4985        TCGA-BP-4986 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BP-4987        TCGA-BP-4988        TCGA-BP-4989        TCGA-BP-4992 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BP-4994        TCGA-BP-4995        TCGA-BP-4998        TCGA-BP-5000 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BP-5001        TCGA-BP-5007        TCGA-BP-5008        TCGA-BP-5009 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-4635        TCGA-CJ-4870        TCGA-CJ-4875        TCGA-CJ-4876 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-4878        TCGA-CJ-4881        TCGA-CJ-4887        TCGA-CJ-4888 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-4889        TCGA-CJ-4890        TCGA-CJ-4891        TCGA-CJ-4895 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-4899        TCGA-CJ-4900        TCGA-CJ-5671        TCGA-CJ-5672 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-5675        TCGA-CJ-5676        TCGA-CJ-5677        TCGA-CJ-5678 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-5679        TCGA-CJ-5680        TCGA-CJ-5681        TCGA-CJ-5682 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-5683        TCGA-CJ-5684        TCGA-CJ-5686        TCGA-CJ-5689 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-6027        TCGA-CJ-6028        TCGA-CJ-6030        TCGA-CJ-6031 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-6032        TCGA-CJ-6033        TCGA-CW-5580        TCGA-CW-5581 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CW-5583        TCGA-CW-5584        TCGA-CW-5585        TCGA-CW-5587 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CW-5588        TCGA-CW-5589        TCGA-CW-5591        TCGA-CW-6087 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CW-6088        TCGA-CW-6090        TCGA-CW-6093        TCGA-CW-6097 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CZ-4854        TCGA-CZ-4857        TCGA-CZ-4858        TCGA-CZ-4860 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CZ-4863        TCGA-CZ-4864        TCGA-CZ-4865        TCGA-CZ-4866 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CZ-5451        TCGA-CZ-5452        TCGA-CZ-5453        TCGA-CZ-5454 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CZ-5455        TCGA-CZ-5456        TCGA-CZ-5457        TCGA-CZ-5458 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CZ-5459        TCGA-CZ-5460        TCGA-CZ-5461        TCGA-CZ-5462 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CZ-5463        TCGA-CZ-5464        TCGA-CZ-5465        TCGA-CZ-5466 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CZ-5467        TCGA-CZ-5468        TCGA-CZ-5470        TCGA-CZ-5982 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CZ-5984        TCGA-CZ-5985        TCGA-CZ-5986        TCGA-CZ-5987 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CZ-5988        TCGA-CZ-5989        TCGA-DV-5565        TCGA-DV-5566 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DV-5567        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5573 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576        TCGA-EU-5904 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 

Clustering(12) Variable = 6q gain
D12V1, multiclass
[1] "Remove cluster labels:" "6Q GAIN CNV"           
clus
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                1                69 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319        TCGA-A3-3320 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324        TCGA-A3-3325 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335        TCGA-A3-3336 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347        TCGA-A3-3349 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359        TCGA-A3-3362 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372        TCGA-A3-3374 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-4644 
"6Q GAIN WILD-TYPE" 
D12V2, multiclass
[1] "Remove cluster labels:" "6Q GAIN CNV"           
clus
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                1                69 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319        TCGA-A3-3320 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324        TCGA-A3-3325 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335        TCGA-A3-3336 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347        TCGA-A3-3349 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359        TCGA-A3-3362 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372        TCGA-A3-3374 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-4644 
"6Q GAIN WILD-TYPE" 
D12V3, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           2               162
  CLUS_2           1               215
  CLUS_3           2               122
D12V4, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           2                97
  CLUS_2           1               118
  CLUS_3           0                71
D12V5, multiclass
D12V6, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           1               185
  CLUS_2           2               150
  CLUS_3           2               107
D12V7, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           2               195
  CLUS_2           1               178
  CLUS_3           2                95
D12V8, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           1                68
  CLUS_2           3               211
  CLUS_3           1               189
D12V9, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           2               113
  CLUS_2           2               189
  CLUS_3           1               168
D12V10, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           1                34
  CLUS_2           1               159
  CLUS_3           3               277
D12V11, multiclass
[1] "Remove cluster labels:" "6Q GAIN CNV"           
clus
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                2               211 
       TCGA-A3-3317        TCGA-A3-3358        TCGA-A3-3387        TCGA-AK-3440 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AK-3458        TCGA-AK-3465        TCGA-B0-4698        TCGA-B0-4700 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B0-4706        TCGA-B0-4710        TCGA-B0-4712        TCGA-B0-4810 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B0-4815        TCGA-B0-4816        TCGA-B0-4818        TCGA-B0-4821 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B0-4833        TCGA-B0-4834        TCGA-B0-4836        TCGA-B0-4837 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B0-4852        TCGA-B0-5075        TCGA-B0-5080        TCGA-B0-5084 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B0-5085        TCGA-B0-5088        TCGA-B0-5399        TCGA-B0-5400 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B0-5402        TCGA-B0-5690        TCGA-B0-5691        TCGA-B0-5692 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B0-5693        TCGA-B0-5694        TCGA-B0-5695        TCGA-B0-5696 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B0-5697        TCGA-B0-5698        TCGA-B0-5699        TCGA-B0-5701 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B0-5702        TCGA-B0-5703        TCGA-B0-5705        TCGA-B0-5706 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B0-5709        TCGA-B0-5710        TCGA-B0-5711        TCGA-B0-5712 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B0-5713        TCGA-B0-5812        TCGA-B2-5633        TCGA-B2-5635 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B2-5639        TCGA-B2-5641        TCGA-B4-5377        TCGA-B4-5378 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835        TCGA-B4-5836 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844        TCGA-B8-4146 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B8-4153        TCGA-B8-4621        TCGA-B8-5545        TCGA-B8-5546 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B8-5549        TCGA-B8-5550        TCGA-B8-5551        TCGA-B8-5552 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B8-5553        TCGA-BP-4173        TCGA-BP-4331        TCGA-BP-4340 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BP-4759        TCGA-BP-4761        TCGA-BP-4770        TCGA-BP-4771 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BP-4787        TCGA-BP-4789        TCGA-BP-4790        TCGA-BP-4797 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BP-4804        TCGA-BP-4807        TCGA-BP-4959        TCGA-BP-4960 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BP-4961        TCGA-BP-4965        TCGA-BP-4967        TCGA-BP-4968 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BP-4969        TCGA-BP-4970        TCGA-BP-4971        TCGA-BP-4973 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BP-4974        TCGA-BP-4975        TCGA-BP-4976        TCGA-BP-4977 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BP-4981        TCGA-BP-4982        TCGA-BP-4985        TCGA-BP-4986 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BP-4987        TCGA-BP-4988        TCGA-BP-4989        TCGA-BP-4992 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BP-4994        TCGA-BP-4995        TCGA-BP-4998        TCGA-BP-5000 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BP-5001        TCGA-BP-5007        TCGA-BP-5008        TCGA-BP-5009 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-4635        TCGA-CJ-4870        TCGA-CJ-4875        TCGA-CJ-4876 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-4878        TCGA-CJ-4881        TCGA-CJ-4887        TCGA-CJ-4888 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-4889        TCGA-CJ-4890        TCGA-CJ-4891        TCGA-CJ-4895 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-4899        TCGA-CJ-4900        TCGA-CJ-5671        TCGA-CJ-5672 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-5675        TCGA-CJ-5676        TCGA-CJ-5677        TCGA-CJ-5678 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-5679        TCGA-CJ-5680        TCGA-CJ-5681        TCGA-CJ-5682 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-5683        TCGA-CJ-5684        TCGA-CJ-5686        TCGA-CJ-5689 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-6027        TCGA-CJ-6028        TCGA-CJ-6030        TCGA-CJ-6031 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-6032        TCGA-CJ-6033        TCGA-CW-5580        TCGA-CW-5581 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CW-5583        TCGA-CW-5584        TCGA-CW-5585        TCGA-CW-5587 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CW-5588        TCGA-CW-5589        TCGA-CW-5591        TCGA-CW-6087 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CW-6088        TCGA-CW-6090        TCGA-CW-6093        TCGA-CW-6097 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CZ-4854        TCGA-CZ-4857        TCGA-CZ-4858        TCGA-CZ-4860 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CZ-4863        TCGA-CZ-4864        TCGA-CZ-4865        TCGA-CZ-4866 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CZ-5451        TCGA-CZ-5452        TCGA-CZ-5453        TCGA-CZ-5454 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CZ-5455        TCGA-CZ-5456        TCGA-CZ-5457        TCGA-CZ-5458 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CZ-5459        TCGA-CZ-5460        TCGA-CZ-5461        TCGA-CZ-5462 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CZ-5463        TCGA-CZ-5464        TCGA-CZ-5465        TCGA-CZ-5466 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CZ-5467        TCGA-CZ-5468        TCGA-CZ-5470        TCGA-CZ-5982 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CZ-5984        TCGA-CZ-5985        TCGA-CZ-5986        TCGA-CZ-5987 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CZ-5988        TCGA-CZ-5989        TCGA-DV-5565        TCGA-DV-5566 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DV-5567        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5573 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576        TCGA-EU-5904 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D12V12, multiclass
[1] "Remove cluster labels:" "6Q GAIN CNV"           
clus
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                2               211 
       TCGA-A3-3317        TCGA-A3-3358        TCGA-A3-3387        TCGA-AK-3440 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AK-3458        TCGA-AK-3465        TCGA-B0-4698        TCGA-B0-4700 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B0-4706        TCGA-B0-4710        TCGA-B0-4712        TCGA-B0-4810 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B0-4815        TCGA-B0-4816        TCGA-B0-4818        TCGA-B0-4821 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B0-4833        TCGA-B0-4834        TCGA-B0-4836        TCGA-B0-4837 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B0-4852        TCGA-B0-5075        TCGA-B0-5080        TCGA-B0-5084 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B0-5085        TCGA-B0-5088        TCGA-B0-5399        TCGA-B0-5400 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B0-5402        TCGA-B0-5690        TCGA-B0-5691        TCGA-B0-5692 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B0-5693        TCGA-B0-5694        TCGA-B0-5695        TCGA-B0-5696 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B0-5697        TCGA-B0-5698        TCGA-B0-5699        TCGA-B0-5701 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B0-5702        TCGA-B0-5703        TCGA-B0-5705        TCGA-B0-5706 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B0-5709        TCGA-B0-5710        TCGA-B0-5711        TCGA-B0-5712 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B0-5713        TCGA-B0-5812        TCGA-B2-5633        TCGA-B2-5635 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B2-5639        TCGA-B2-5641        TCGA-B4-5377        TCGA-B4-5378 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835        TCGA-B4-5836 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844        TCGA-B8-4146 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B8-4153        TCGA-B8-4621        TCGA-B8-5545        TCGA-B8-5546 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B8-5549        TCGA-B8-5550        TCGA-B8-5551        TCGA-B8-5552 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B8-5553        TCGA-BP-4173        TCGA-BP-4331        TCGA-BP-4340 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BP-4759        TCGA-BP-4761        TCGA-BP-4770        TCGA-BP-4771 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BP-4787        TCGA-BP-4789        TCGA-BP-4790        TCGA-BP-4797 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BP-4804        TCGA-BP-4807        TCGA-BP-4959        TCGA-BP-4960 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BP-4961        TCGA-BP-4965        TCGA-BP-4967        TCGA-BP-4968 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BP-4969        TCGA-BP-4970        TCGA-BP-4971        TCGA-BP-4973 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BP-4974        TCGA-BP-4975        TCGA-BP-4976        TCGA-BP-4977 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BP-4981        TCGA-BP-4982        TCGA-BP-4985        TCGA-BP-4986 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BP-4987        TCGA-BP-4988        TCGA-BP-4989        TCGA-BP-4992 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BP-4994        TCGA-BP-4995        TCGA-BP-4998        TCGA-BP-5000 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BP-5001        TCGA-BP-5007        TCGA-BP-5008        TCGA-BP-5009 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-4635        TCGA-CJ-4870        TCGA-CJ-4875        TCGA-CJ-4876 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-4878        TCGA-CJ-4881        TCGA-CJ-4887        TCGA-CJ-4888 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-4889        TCGA-CJ-4890        TCGA-CJ-4891        TCGA-CJ-4895 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-4899        TCGA-CJ-4900        TCGA-CJ-5671        TCGA-CJ-5672 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-5675        TCGA-CJ-5676        TCGA-CJ-5677        TCGA-CJ-5678 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-5679        TCGA-CJ-5680        TCGA-CJ-5681        TCGA-CJ-5682 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-5683        TCGA-CJ-5684        TCGA-CJ-5686        TCGA-CJ-5689 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-6027        TCGA-CJ-6028        TCGA-CJ-6030        TCGA-CJ-6031 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-6032        TCGA-CJ-6033        TCGA-CW-5580        TCGA-CW-5581 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CW-5583        TCGA-CW-5584        TCGA-CW-5585        TCGA-CW-5587 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CW-5588        TCGA-CW-5589        TCGA-CW-5591        TCGA-CW-6087 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CW-6088        TCGA-CW-6090        TCGA-CW-6093        TCGA-CW-6097 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CZ-4854        TCGA-CZ-4857        TCGA-CZ-4858        TCGA-CZ-4860 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CZ-4863        TCGA-CZ-4864        TCGA-CZ-4865        TCGA-CZ-4866 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CZ-5451        TCGA-CZ-5452        TCGA-CZ-5453        TCGA-CZ-5454 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CZ-5455        TCGA-CZ-5456        TCGA-CZ-5457        TCGA-CZ-5458 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CZ-5459        TCGA-CZ-5460        TCGA-CZ-5461        TCGA-CZ-5462 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CZ-5463        TCGA-CZ-5464        TCGA-CZ-5465        TCGA-CZ-5466 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CZ-5467        TCGA-CZ-5468        TCGA-CZ-5470        TCGA-CZ-5982 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CZ-5984        TCGA-CZ-5985        TCGA-CZ-5986        TCGA-CZ-5987 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CZ-5988        TCGA-CZ-5989        TCGA-DV-5565        TCGA-DV-5566 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DV-5567        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5573 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576        TCGA-EU-5904 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 

Clustering(13) Variable = 7p gain
D13V1, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           8                25
  CLUS_2           6                18
  CLUS_3           4                 9
D13V2, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           4                10
  CLUS_2           8                24
  CLUS_3           6                18
D13V3, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          69                95
  CLUS_2          29               187
  CLUS_3          30                94
D13V4, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          29                70
  CLUS_2          19               100
  CLUS_3          12                59
D13V5, multiclass
D13V6, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          34               152
  CLUS_2          46               106
  CLUS_3          36                73
D13V7, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          43               154
  CLUS_2          57               122
  CLUS_3          22                75
D13V8, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          12                57
  CLUS_2          52               162
  CLUS_3          58               132
D13V9, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          22                93
  CLUS_2          47               144
  CLUS_3          56               113
D13V10, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          11                24
  CLUS_2          43               117
  CLUS_3          71               209
D13V11, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          10                40
  CLUS_2          17                72
  CLUS_3          28                46
D13V12, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          19                38
  CLUS_2          20                72
  CLUS_3          16                48

Clustering(14) Variable = 7q gain
D14V1, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           8                25
  CLUS_2           6                18
  CLUS_3           4                 9
D14V2, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           4                10
  CLUS_2           8                24
  CLUS_3           6                18
D14V3, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          69                95
  CLUS_2          29               187
  CLUS_3          32                92
D14V4, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          31                68
  CLUS_2          20                99
  CLUS_3          13                58
D14V5, multiclass
D14V6, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          32               154
  CLUS_2          49               103
  CLUS_3          37                72
D14V7, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          43               154
  CLUS_2          58               121
  CLUS_3          23                74
D14V8, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          14                55
  CLUS_2          51               163
  CLUS_3          59               131
D14V9, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          22                93
  CLUS_2          47               144
  CLUS_3          58               111
D14V10, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          12                23
  CLUS_2          44               116
  CLUS_3          71               209
D14V11, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          10                40
  CLUS_2          17                72
  CLUS_3          30                44
D14V12, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          21                36
  CLUS_2          19                73
  CLUS_3          17                47

Clustering(15) Variable = 8p gain
D15V1, multiclass
[1] "Remove cluster labels:" "8P GAIN CNV"           
clus
      8P GAIN CNV 8P GAIN WILD-TYPE 
                2                68 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3317        TCGA-A3-3319        TCGA-A3-3320        TCGA-A3-3322 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3323        TCGA-A3-3324        TCGA-A3-3325        TCGA-A3-3326 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3331        TCGA-A3-3335        TCGA-A3-3336        TCGA-A3-3343 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3346        TCGA-A3-3347        TCGA-A3-3349        TCGA-A3-3351 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3352        TCGA-A3-3359        TCGA-A3-3362        TCGA-A3-3363 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3365        TCGA-A3-3372        TCGA-A3-3374        TCGA-A3-3378 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383        TCGA-AK-3426 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443        TCGA-AK-3444 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455        TCGA-AK-3456 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778        TCGA-B2-3923 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099        TCGA-B2-4102 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151        TCGA-B8-4154 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161        TCGA-BP-4162 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167        TCGA-CJ-4634 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638        TCGA-CJ-4639 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643        TCGA-CJ-4644 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
D15V2, multiclass
[1] "Remove cluster labels:" "8P GAIN CNV"           
clus
      8P GAIN CNV 8P GAIN WILD-TYPE 
                2                68 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3317        TCGA-A3-3319        TCGA-A3-3320        TCGA-A3-3322 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3323        TCGA-A3-3324        TCGA-A3-3325        TCGA-A3-3326 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3331        TCGA-A3-3335        TCGA-A3-3336        TCGA-A3-3343 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3346        TCGA-A3-3347        TCGA-A3-3349        TCGA-A3-3351 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3352        TCGA-A3-3359        TCGA-A3-3362        TCGA-A3-3363 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3365        TCGA-A3-3372        TCGA-A3-3374        TCGA-A3-3378 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383        TCGA-AK-3426 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443        TCGA-AK-3444 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455        TCGA-AK-3456 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778        TCGA-B2-3923 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099        TCGA-B2-4102 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151        TCGA-B8-4154 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161        TCGA-BP-4162 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167        TCGA-CJ-4634 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638        TCGA-CJ-4639 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643        TCGA-CJ-4644 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
D15V3, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          13               151
  CLUS_2           0               216
  CLUS_3           3               121
D15V4, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           8                91
  CLUS_2           2               117
  CLUS_3           2                69
D15V5, multiclass
D15V6, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           2               184
  CLUS_2           7               145
  CLUS_3           3               106
D15V7, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           0               197
  CLUS_2          10               169
  CLUS_3           3                94
D15V8, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           3                66
  CLUS_2           0               214
  CLUS_3          10               180
D15V9, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           2               113
  CLUS_2           1               190
  CLUS_3          11               158
D15V10, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           2                33
  CLUS_2           7               153
  CLUS_3           5               275
D15V11, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           0                50
  CLUS_2           0                89
  CLUS_3           6                68
D15V12, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           3                54
  CLUS_2           0                92
  CLUS_3           3                61

Clustering(16) Variable = 8q gain
D16V1, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           0                33
  CLUS_2           2                22
  CLUS_3           2                11
D16V2, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           2                12
  CLUS_2           0                32
  CLUS_3           2                22
D16V3, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          27               137
  CLUS_2           0               216
  CLUS_3           9               115
D16V4, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          15                84
  CLUS_2           2               117
  CLUS_3           5                66
D16V5, multiclass
D16V6, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           7               179
  CLUS_2          14               138
  CLUS_3          11                98
D16V7, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           1               196
  CLUS_2          25               154
  CLUS_3           5                92
D16V8, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           3                66
  CLUS_2           4               210
  CLUS_3          24               166
D16V9, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           6               109
  CLUS_2           3               188
  CLUS_3          24               145
D16V10, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           4                31
  CLUS_2          17               143
  CLUS_3          12               268
D16V11, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           0                50
  CLUS_2           0                89
  CLUS_3          12                62
D16V12, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           9                48
  CLUS_2           0                92
  CLUS_3           3                61

Clustering(17) Variable = 9p gain
D17V1, multiclass
[1] "Remove cluster labels:" "9P GAIN CNV"           
clus
      9P GAIN CNV 9P GAIN WILD-TYPE 
                1                69 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CJ-4644 
"9P GAIN WILD-TYPE" 
D17V2, multiclass
[1] "Remove cluster labels:" "9P GAIN CNV"           
clus
      9P GAIN CNV 9P GAIN WILD-TYPE 
                1                69 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CJ-4644 
"9P GAIN WILD-TYPE" 
D17V3, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           1               163
  CLUS_2           4               212
  CLUS_3           3               121
D17V4, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           1                98
  CLUS_2           2               117
  CLUS_3           0                71
D17V5, multiclass
D17V6, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           4               182
  CLUS_2           0               152
  CLUS_3           2               107
D17V7, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           4               193
  CLUS_2           0               179
  CLUS_3           2                95
D17V8, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           2                67
  CLUS_2           4               210
  CLUS_3           0               190
D17V9, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           2               113
  CLUS_2           4               187
  CLUS_3           2               167
D17V10, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           2                33
  CLUS_2           0               160
  CLUS_3           6               274
D17V11, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           3                47
  CLUS_2           1                88
  CLUS_3           0                74
D17V12, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           0                57
  CLUS_2           2                90
  CLUS_3           2                62

Clustering(18) Variable = 9q gain
D18V1, multiclass
[1] "Remove cluster labels:" "9Q GAIN CNV"           
clus
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                1                69 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CJ-4644 
"9Q GAIN WILD-TYPE" 
D18V2, multiclass
[1] "Remove cluster labels:" "9Q GAIN CNV"           
clus
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                1                69 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CJ-4644 
"9Q GAIN WILD-TYPE" 
D18V3, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           1               163
  CLUS_2           2               214
  CLUS_3           5               119
D18V4, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           3                96
  CLUS_2           1               118
  CLUS_3           1                70
D18V5, multiclass
D18V6, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           2               184
  CLUS_2           1               151
  CLUS_3           3               106
D18V7, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           3               194
  CLUS_2           2               177
  CLUS_3           3                94
D18V8, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           2                67
  CLUS_2           3               211
  CLUS_3           3               187
D18V9, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           2               113
  CLUS_2           2               189
  CLUS_3           4               165
D18V10, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           2                33
  CLUS_2           2               158
  CLUS_3           4               276
D18V11, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           2                48
  CLUS_2           0                89
  CLUS_3           2                72
D18V12, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           1                56
  CLUS_2           1                91
  CLUS_3           2                62

Clustering(19) Variable = 10p gain
D19V1, multiclass
[1] "Remove cluster labels:" "10P GAIN CNV"          
clus
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3374         TCGA-A3-3378 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3380         TCGA-A3-3382         TCGA-A3-3383 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3427         TCGA-AK-3440 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AK-3443         TCGA-AK-3444         TCGA-AK-3447 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AK-3455         TCGA-AK-3456         TCGA-AK-3465 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
D19V2, multiclass
[1] "Remove cluster labels:" "10P GAIN CNV"          
clus
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3374         TCGA-A3-3378 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3380         TCGA-A3-3382         TCGA-A3-3383 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3427         TCGA-AK-3440 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AK-3443         TCGA-AK-3444         TCGA-AK-3447 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AK-3455         TCGA-AK-3456         TCGA-AK-3465 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
D19V3, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            3                161
  CLUS_2            1                215
  CLUS_3            2                122
D19V4, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            1                 98
  CLUS_2            2                117
  CLUS_3            1                 70
D19V5, multiclass
D19V6, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            2                184
  CLUS_2            2                150
  CLUS_3            1                108
D19V7, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            1                196
  CLUS_2            4                175
  CLUS_3            1                 96
D19V8, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            1                 68
  CLUS_2            1                213
  CLUS_3            4                186
D19V9, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            1                114
  CLUS_2            2                189
  CLUS_3            3                166
D19V10, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            1                 34
  CLUS_2            1                159
  CLUS_3            4                276
D19V11, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            1                 49
  CLUS_2            1                 88
  CLUS_3            1                 73
D19V12, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            1                 56
  CLUS_2            1                 91
  CLUS_3            1                 63

Clustering(20) Variable = 10q gain
D20V1, multiclass
[1] "Remove cluster labels:" "10Q GAIN CNV"          
clus
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3374         TCGA-A3-3378 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3380         TCGA-A3-3382         TCGA-A3-3383 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3427         TCGA-AK-3440 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AK-3443         TCGA-AK-3444         TCGA-AK-3447 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AK-3455         TCGA-AK-3456         TCGA-AK-3465 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D20V2, multiclass
[1] "Remove cluster labels:" "10Q GAIN CNV"          
clus
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3374         TCGA-A3-3378 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3380         TCGA-A3-3382         TCGA-A3-3383 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3427         TCGA-AK-3440 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AK-3443         TCGA-AK-3444         TCGA-AK-3447 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AK-3455         TCGA-AK-3456         TCGA-AK-3465 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D20V3, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            2                162
  CLUS_2            0                216
  CLUS_3            2                122
D20V4, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            1                 98
  CLUS_2            1                118
  CLUS_3            1                 70
D20V5, multiclass
D20V6, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            1                185
  CLUS_2            2                150
  CLUS_3            0                109
D20V7, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            1                196
  CLUS_2            2                177
  CLUS_3            1                 96
D20V8, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            1                 68
  CLUS_2            1                213
  CLUS_3            2                188
D20V9, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            1                114
  CLUS_2            1                190
  CLUS_3            2                167
D20V10, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            1                 34
  CLUS_2            1                159
  CLUS_3            2                278
D20V11, multiclass
[1] "Remove cluster labels:" "10Q GAIN CNV"          
clus
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 2                211 
        TCGA-A3-3317         TCGA-A3-3358         TCGA-A3-3387 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AK-3440         TCGA-AK-3458         TCGA-AK-3465 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-4698         TCGA-B0-4700         TCGA-B0-4706 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-4710         TCGA-B0-4712         TCGA-B0-4810 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-4811         TCGA-B0-4815         TCGA-B0-4816 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-4818         TCGA-B0-4821         TCGA-B0-4833 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-4834         TCGA-B0-4836         TCGA-B0-4837 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-4852         TCGA-B0-5075         TCGA-B0-5080 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-5084         TCGA-B0-5085         TCGA-B0-5088 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-5399         TCGA-B0-5400         TCGA-B0-5402 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-5690         TCGA-B0-5691         TCGA-B0-5692 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-5693         TCGA-B0-5694         TCGA-B0-5695 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-5696         TCGA-B0-5697         TCGA-B0-5698 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-5699         TCGA-B0-5701         TCGA-B0-5702 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-5703         TCGA-B0-5705         TCGA-B0-5706 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-5709         TCGA-B0-5710         TCGA-B0-5711 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-5712         TCGA-B0-5713         TCGA-B0-5812 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B2-5633         TCGA-B2-5635         TCGA-B2-5639 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B2-5641         TCGA-B4-5377         TCGA-B4-5378 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B4-5832         TCGA-B4-5834         TCGA-B4-5835 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B4-5836         TCGA-B4-5838         TCGA-B4-5843 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B4-5844         TCGA-B8-4146         TCGA-B8-4153 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B8-4621         TCGA-B8-5545         TCGA-B8-5546 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B8-5549         TCGA-B8-5550         TCGA-B8-5551 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B8-5552         TCGA-B8-5553         TCGA-BP-4173 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4331         TCGA-BP-4340         TCGA-BP-4759 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4761         TCGA-BP-4770         TCGA-BP-4771 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4787         TCGA-BP-4789         TCGA-BP-4790 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4797         TCGA-BP-4804         TCGA-BP-4807 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4959         TCGA-BP-4960         TCGA-BP-4961 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4965         TCGA-BP-4967         TCGA-BP-4968 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4969         TCGA-BP-4970         TCGA-BP-4971 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4973         TCGA-BP-4974         TCGA-BP-4975 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4976         TCGA-BP-4977         TCGA-BP-4981 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4982         TCGA-BP-4985         TCGA-BP-4986 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4987         TCGA-BP-4988         TCGA-BP-4989 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4992         TCGA-BP-4994         TCGA-BP-4995 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4998         TCGA-BP-5000         TCGA-BP-5001 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-5007         TCGA-BP-5008         TCGA-BP-5009 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-4635         TCGA-CJ-4870         TCGA-CJ-4875 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-4876         TCGA-CJ-4878         TCGA-CJ-4881 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-4887         TCGA-CJ-4888         TCGA-CJ-4889 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-4890         TCGA-CJ-4891         TCGA-CJ-4895 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-4899         TCGA-CJ-4900         TCGA-CJ-5671 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-5672         TCGA-CJ-5675         TCGA-CJ-5676 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-5677         TCGA-CJ-5678         TCGA-CJ-5679 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-5680         TCGA-CJ-5681         TCGA-CJ-5682 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-5683         TCGA-CJ-5684         TCGA-CJ-5686 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-5689         TCGA-CJ-6027         TCGA-CJ-6028 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-6030         TCGA-CJ-6031         TCGA-CJ-6032 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-6033         TCGA-CW-5580         TCGA-CW-5581 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CW-5583         TCGA-CW-5584         TCGA-CW-5585 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CW-5587         TCGA-CW-5588         TCGA-CW-5589 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CW-5591         TCGA-CW-6087         TCGA-CW-6088 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CW-6090         TCGA-CW-6093         TCGA-CW-6097 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CZ-4854         TCGA-CZ-4857         TCGA-CZ-4858 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CZ-4860         TCGA-CZ-4863         TCGA-CZ-4864 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CZ-4865         TCGA-CZ-4866         TCGA-CZ-5451 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CZ-5452         TCGA-CZ-5453         TCGA-CZ-5454 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CZ-5455         TCGA-CZ-5456         TCGA-CZ-5457 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CZ-5458         TCGA-CZ-5459         TCGA-CZ-5460 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CZ-5461         TCGA-CZ-5462         TCGA-CZ-5463 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CZ-5464         TCGA-CZ-5465         TCGA-CZ-5466 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CZ-5467         TCGA-CZ-5469         TCGA-CZ-5470 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CZ-5982         TCGA-CZ-5984         TCGA-CZ-5985 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CZ-5986         TCGA-CZ-5987         TCGA-CZ-5988 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CZ-5989         TCGA-DV-5565         TCGA-DV-5566 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DV-5567         TCGA-DV-5568         TCGA-DV-5569 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DV-5573         TCGA-DV-5574         TCGA-DV-5575 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DV-5576         TCGA-EU-5904         TCGA-EU-5906 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EU-5907 
"10Q GAIN WILD-TYPE" 
D20V12, multiclass
[1] "Remove cluster labels:" "10Q GAIN CNV"          
clus
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 2                211 
        TCGA-A3-3317         TCGA-A3-3358         TCGA-A3-3387 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AK-3440         TCGA-AK-3458         TCGA-AK-3465 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-4698         TCGA-B0-4700         TCGA-B0-4706 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-4710         TCGA-B0-4712         TCGA-B0-4810 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-4811         TCGA-B0-4815         TCGA-B0-4816 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-4818         TCGA-B0-4821         TCGA-B0-4833 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-4834         TCGA-B0-4836         TCGA-B0-4837 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-4852         TCGA-B0-5075         TCGA-B0-5080 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-5084         TCGA-B0-5085         TCGA-B0-5088 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-5399         TCGA-B0-5400         TCGA-B0-5402 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-5690         TCGA-B0-5691         TCGA-B0-5692 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-5693         TCGA-B0-5694         TCGA-B0-5695 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-5696         TCGA-B0-5697         TCGA-B0-5698 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-5699         TCGA-B0-5701         TCGA-B0-5702 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-5703         TCGA-B0-5705         TCGA-B0-5706 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-5709         TCGA-B0-5710         TCGA-B0-5711 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B0-5712         TCGA-B0-5713         TCGA-B0-5812 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B2-5633         TCGA-B2-5635         TCGA-B2-5639 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B2-5641         TCGA-B4-5377         TCGA-B4-5378 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B4-5832         TCGA-B4-5834         TCGA-B4-5835 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B4-5836         TCGA-B4-5838         TCGA-B4-5843 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B4-5844         TCGA-B8-4146         TCGA-B8-4153 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B8-4621         TCGA-B8-5545         TCGA-B8-5546 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B8-5549         TCGA-B8-5550         TCGA-B8-5551 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B8-5552         TCGA-B8-5553         TCGA-BP-4173 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4331         TCGA-BP-4340         TCGA-BP-4759 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4761         TCGA-BP-4770         TCGA-BP-4771 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4787         TCGA-BP-4789         TCGA-BP-4790 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4797         TCGA-BP-4804         TCGA-BP-4807 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4959         TCGA-BP-4960         TCGA-BP-4961 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4965         TCGA-BP-4967         TCGA-BP-4968 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4969         TCGA-BP-4970         TCGA-BP-4971 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4973         TCGA-BP-4974         TCGA-BP-4975 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4976         TCGA-BP-4977         TCGA-BP-4981 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4982         TCGA-BP-4985         TCGA-BP-4986 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4987         TCGA-BP-4988         TCGA-BP-4989 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4992         TCGA-BP-4994         TCGA-BP-4995 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4998         TCGA-BP-5000         TCGA-BP-5001 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-5007         TCGA-BP-5008         TCGA-BP-5009 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-4635         TCGA-CJ-4870         TCGA-CJ-4875 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-4876         TCGA-CJ-4878         TCGA-CJ-4881 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-4887         TCGA-CJ-4888         TCGA-CJ-4889 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-4890         TCGA-CJ-4891         TCGA-CJ-4895 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-4899         TCGA-CJ-4900         TCGA-CJ-5671 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-5672         TCGA-CJ-5675         TCGA-CJ-5676 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-5677         TCGA-CJ-5678         TCGA-CJ-5679 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-5680         TCGA-CJ-5681         TCGA-CJ-5682 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-5683         TCGA-CJ-5684         TCGA-CJ-5686 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-5689         TCGA-CJ-6027         TCGA-CJ-6028 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-6030         TCGA-CJ-6031         TCGA-CJ-6032 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-6033         TCGA-CW-5580         TCGA-CW-5581 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CW-5583         TCGA-CW-5584         TCGA-CW-5585 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CW-5587         TCGA-CW-5588         TCGA-CW-5589 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CW-5591         TCGA-CW-6087         TCGA-CW-6088 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CW-6090         TCGA-CW-6093         TCGA-CW-6097 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CZ-4854         TCGA-CZ-4857         TCGA-CZ-4858 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CZ-4860         TCGA-CZ-4863         TCGA-CZ-4864 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CZ-4865         TCGA-CZ-4866         TCGA-CZ-5451 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CZ-5452         TCGA-CZ-5453         TCGA-CZ-5454 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CZ-5455         TCGA-CZ-5456         TCGA-CZ-5457 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CZ-5458         TCGA-CZ-5459         TCGA-CZ-5460 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CZ-5461         TCGA-CZ-5462         TCGA-CZ-5463 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CZ-5464         TCGA-CZ-5465         TCGA-CZ-5466 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CZ-5467         TCGA-CZ-5469         TCGA-CZ-5470 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CZ-5982         TCGA-CZ-5984         TCGA-CZ-5985 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CZ-5986         TCGA-CZ-5987         TCGA-CZ-5988 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CZ-5989         TCGA-DV-5565         TCGA-DV-5566 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DV-5567         TCGA-DV-5568         TCGA-DV-5569 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DV-5573         TCGA-DV-5574         TCGA-DV-5575 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DV-5576         TCGA-EU-5904         TCGA-EU-5906 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EU-5907 
"10Q GAIN WILD-TYPE" 

Clustering(21) Variable = 11p gain
D21V1, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            1                 32
  CLUS_2            1                 23
  CLUS_3            1                 12
D21V2, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            1                 13
  CLUS_2            1                 31
  CLUS_3            1                 23
D21V3, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            9                155
  CLUS_2            2                214
  CLUS_3            6                118
D21V4, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            4                 95
  CLUS_2            5                114
  CLUS_3            1                 70
D21V5, multiclass
D21V6, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            5                181
  CLUS_2            4                148
  CLUS_3            6                103
D21V7, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            4                193
  CLUS_2            7                172
  CLUS_3            4                 93
D21V8, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            2                 67
  CLUS_2            4                210
  CLUS_3            9                181
D21V9, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            4                111
  CLUS_2            6                185
  CLUS_3            7                162
D21V10, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            2                 33
  CLUS_2            7                153
  CLUS_3            8                272
D21V11, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            2                 48
  CLUS_2            1                 88
  CLUS_3            4                 70
D21V12, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            2                 55
  CLUS_2            2                 90
  CLUS_3            3                 61

Clustering(22) Variable = 11q gain
D22V1, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            1                 32
  CLUS_2            1                 23
  CLUS_3            1                 12
D22V2, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            1                 13
  CLUS_2            1                 31
  CLUS_3            1                 23
D22V3, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            7                157
  CLUS_2            2                214
  CLUS_3            6                118
D22V4, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            3                 96
  CLUS_2            5                114
  CLUS_3            1                 70
D22V5, multiclass
D22V6, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            5                181
  CLUS_2            3                149
  CLUS_3            5                104
D22V7, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            4                193
  CLUS_2            5                174
  CLUS_3            4                 93
D22V8, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            2                 67
  CLUS_2            4                210
  CLUS_3            7                183
D22V9, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            3                112
  CLUS_2            6                185
  CLUS_3            6                163
D22V10, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            2                 33
  CLUS_2            6                154
  CLUS_3            7                273
D22V11, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            2                 48
  CLUS_2            1                 88
  CLUS_3            2                 72
D22V12, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            1                 56
  CLUS_2            2                 90
  CLUS_3            2                 62

Clustering(23) Variable = 12p gain
D23V1, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            2                 31
  CLUS_2            5                 19
  CLUS_3            1                 12
D23V2, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            1                 13
  CLUS_2            2                 30
  CLUS_3            5                 19
D23V3, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           48                116
  CLUS_2           14                202
  CLUS_3           18                106
D23V4, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           29                 70
  CLUS_2           13                106
  CLUS_3           13                 58
D23V5, multiclass
D23V6, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           18                168
  CLUS_2           29                123
  CLUS_3           22                 87
D23V7, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           15                182
  CLUS_2           45                134
  CLUS_3           12                 85
D23V8, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            7                 62
  CLUS_2           18                196
  CLUS_3           47                143
D23V9, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           13                102
  CLUS_2           18                173
  CLUS_3           47                122
D23V10, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            6                 29
  CLUS_2           29                131
  CLUS_3           43                237
D23V11, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            5                 45
  CLUS_2            4                 85
  CLUS_3           24                 50
D23V12, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           18                 39
  CLUS_2            8                 84
  CLUS_3            7                 57

Clustering(24) Variable = 12q gain
D24V1, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            2                 31
  CLUS_2            5                 19
  CLUS_3            1                 12
D24V2, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            1                 13
  CLUS_2            2                 30
  CLUS_3            5                 19
D24V3, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1           49                115
  CLUS_2           14                202
  CLUS_3           18                106
D24V4, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1           29                 70
  CLUS_2           13                106
  CLUS_3           13                 58
D24V5, multiclass
D24V6, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1           18                168
  CLUS_2           30                122
  CLUS_3           22                 87
D24V7, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1           15                182
  CLUS_2           46                133
  CLUS_3           12                 85
D24V8, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            7                 62
  CLUS_2           18                196
  CLUS_3           48                142
D24V9, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1           13                102
  CLUS_2           18                173
  CLUS_3           48                121
D24V10, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            6                 29
  CLUS_2           30                130
  CLUS_3           43                237
D24V11, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            5                 45
  CLUS_2            4                 85
  CLUS_3           25                 49
D24V12, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1           19                 38
  CLUS_2            8                 84
  CLUS_3            7                 57

Clustering(25) Variable = 13q gain
D25V1, multiclass
[1] "Remove cluster labels:" "13Q GAIN CNV"          
clus
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3374         TCGA-A3-3378 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3380         TCGA-A3-3382         TCGA-A3-3383 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3427         TCGA-AK-3440 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AK-3443         TCGA-AK-3444         TCGA-AK-3447 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AK-3455         TCGA-AK-3456         TCGA-AK-3465 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D25V2, multiclass
[1] "Remove cluster labels:" "13Q GAIN CNV"          
clus
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3374         TCGA-A3-3378 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3380         TCGA-A3-3382         TCGA-A3-3383 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3427         TCGA-AK-3440 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AK-3443         TCGA-AK-3444         TCGA-AK-3447 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AK-3455         TCGA-AK-3456         TCGA-AK-3465 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D25V3, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            5                159
  CLUS_2            5                211
  CLUS_3            4                120
D25V4, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            7                 92
  CLUS_2            6                113
  CLUS_3            0                 71
D25V5, multiclass
D25V6, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            7                179
  CLUS_2            4                148
  CLUS_3            2                107
D25V7, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            3                194
  CLUS_2            4                175
  CLUS_3            6                 91
D25V8, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            3                 66
  CLUS_2            5                209
  CLUS_3            5                185
D25V9, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            5                110
  CLUS_2            5                186
  CLUS_3            4                165
D25V10, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            1                 34
  CLUS_2            4                156
  CLUS_3            9                271
D25V11, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            2                 48
  CLUS_2            4                 85
  CLUS_3            2                 72
D25V12, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            1                 56
  CLUS_2            4                 88
  CLUS_3            3                 61

Clustering(26) Variable = 14q gain
D26V1, multiclass
[1] "Remove cluster labels:" "14Q GAIN CNV"          
clus
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3378         TCGA-A3-3380 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3382         TCGA-A3-3383         TCGA-AK-3426 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AK-3427         TCGA-AK-3440         TCGA-AK-3443 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AK-3444         TCGA-AK-3447         TCGA-AK-3453 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AK-3455         TCGA-AK-3456         TCGA-AK-3465 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
D26V2, multiclass
[1] "Remove cluster labels:" "14Q GAIN CNV"          
clus
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3378         TCGA-A3-3380 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3382         TCGA-A3-3383         TCGA-AK-3426 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AK-3427         TCGA-AK-3440         TCGA-AK-3443 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AK-3444         TCGA-AK-3447         TCGA-AK-3453 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AK-3455         TCGA-AK-3456         TCGA-AK-3465 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
D26V3, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            2                162
  CLUS_2            0                216
  CLUS_3            3                121
D26V4, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            2                 97
  CLUS_2            1                118
  CLUS_3            0                 71
D26V5, multiclass
D26V6, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            1                185
  CLUS_2            0                152
  CLUS_3            3                106
D26V7, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            0                197
  CLUS_2            1                178
  CLUS_3            4                 93
D26V8, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            2                 67
  CLUS_2            0                214
  CLUS_3            3                187
D26V9, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            1                114
  CLUS_2            0                191
  CLUS_3            4                165
D26V10, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            2                 33
  CLUS_2            3                157
  CLUS_3            0                280
D26V11, multiclass
D26V12, multiclass

Clustering(27) Variable = 15q gain
D27V1, multiclass
[1] "Remove cluster labels:" "15Q GAIN CNV"          
clus
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 2                 68 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3378         TCGA-A3-3380         TCGA-A3-3382 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3383         TCGA-AK-3426         TCGA-AK-3427 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AK-3440         TCGA-AK-3443         TCGA-AK-3444 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AK-3447         TCGA-AK-3453         TCGA-AK-3455 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AK-3456         TCGA-AK-3465         TCGA-AS-3777 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AS-3778         TCGA-B2-3923         TCGA-B2-3924 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B2-4098         TCGA-B2-4099         TCGA-B2-4102 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B8-4143         TCGA-B8-4148         TCGA-B8-4151 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B8-4154         TCGA-B8-4619         TCGA-B8-4620 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BP-4161         TCGA-BP-4162         TCGA-BP-4163 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BP-4164         TCGA-BP-4167         TCGA-CJ-4634 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CJ-4636         TCGA-CJ-4637         TCGA-CJ-4638 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CJ-4639         TCGA-CJ-4640         TCGA-CJ-4641 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CJ-4643         TCGA-CJ-4644 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
D27V2, multiclass
[1] "Remove cluster labels:" "15Q GAIN CNV"          
clus
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 2                 68 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3378         TCGA-A3-3380         TCGA-A3-3382 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3383         TCGA-AK-3426         TCGA-AK-3427 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AK-3440         TCGA-AK-3443         TCGA-AK-3444 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AK-3447         TCGA-AK-3453         TCGA-AK-3455 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AK-3456         TCGA-AK-3465         TCGA-AS-3777 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AS-3778         TCGA-B2-3923         TCGA-B2-3924 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B2-4098         TCGA-B2-4099         TCGA-B2-4102 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B8-4143         TCGA-B8-4148         TCGA-B8-4151 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B8-4154         TCGA-B8-4619         TCGA-B8-4620 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BP-4161         TCGA-BP-4162         TCGA-BP-4163 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BP-4164         TCGA-BP-4167         TCGA-CJ-4634 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CJ-4636         TCGA-CJ-4637         TCGA-CJ-4638 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CJ-4639         TCGA-CJ-4640         TCGA-CJ-4641 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CJ-4643         TCGA-CJ-4644 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
D27V3, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            6                158
  CLUS_2            2                214
  CLUS_3            6                118
D27V4, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            1                 98
  CLUS_2            4                115
  CLUS_3            1                 70
D27V5, multiclass
D27V6, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            2                184
  CLUS_2            5                147
  CLUS_3            4                105
D27V7, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            5                192
  CLUS_2            2                177
  CLUS_3            5                 92
D27V8, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            3                 66
  CLUS_2            6                208
  CLUS_3            3                187
D27V9, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            4                111
  CLUS_2            6                185
  CLUS_3            4                165
D27V10, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            2                 33
  CLUS_2            4                156
  CLUS_3            8                272
D27V11, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            1                 49
  CLUS_2            2                 87
  CLUS_3            0                 74
D27V12, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            1                 56
  CLUS_2            2                 90
  CLUS_3            0                 64

Clustering(28) Variable = 16p gain
D28V1, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            2                 31
  CLUS_2            6                 18
  CLUS_3            1                 12
D28V2, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            2                 12
  CLUS_2            2                 30
  CLUS_3            5                 19
D28V3, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           30                134
  CLUS_2           24                192
  CLUS_3           14                110
D28V4, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           11                 88
  CLUS_2           18                101
  CLUS_3            8                 63
D28V5, multiclass
D28V6, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           17                169
  CLUS_2           27                125
  CLUS_3           14                 95
D28V7, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           24                173
  CLUS_2           28                151
  CLUS_3           13                 84
D28V8, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           15                 54
  CLUS_2           25                189
  CLUS_3           25                165
D28V9, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           10                105
  CLUS_2           27                164
  CLUS_3           28                141
D28V10, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            6                 29
  CLUS_2           19                141
  CLUS_3           40                240
D28V11, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            4                 46
  CLUS_2           12                 77
  CLUS_3           17                 57
D28V12, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           13                 44
  CLUS_2           13                 79
  CLUS_3            7                 57

Clustering(29) Variable = 16q gain
D29V1, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            1                 32
  CLUS_2            5                 19
  CLUS_3            1                 12
D29V2, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            2                 12
  CLUS_2            1                 31
  CLUS_3            4                 20
D29V3, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           27                137
  CLUS_2           20                196
  CLUS_3           14                110
D29V4, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           11                 88
  CLUS_2           15                104
  CLUS_3            7                 64
D29V5, multiclass
D29V6, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           15                171
  CLUS_2           23                129
  CLUS_3           13                 96
D29V7, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           22                175
  CLUS_2           25                154
  CLUS_3           11                 86
D29V8, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           12                 57
  CLUS_2           23                191
  CLUS_3           23                167
D29V9, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           10                105
  CLUS_2           22                169
  CLUS_3           26                143
D29V10, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            5                 30
  CLUS_2           19                141
  CLUS_3           34                246
D29V11, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            4                 46
  CLUS_2            9                 80
  CLUS_3           16                 58
D29V12, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           11                 46
  CLUS_2           11                 81
  CLUS_3            7                 57

Clustering(30) Variable = 17p gain
D30V1, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            0                 33
  CLUS_2            0                 24
  CLUS_3            3                 10
D30V2, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            3                 11
  CLUS_2            0                 32
  CLUS_3            0                 24
D30V3, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            9                155
  CLUS_2            1                215
  CLUS_3            6                118
D30V4, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            2                 97
  CLUS_2            5                114
  CLUS_3            4                 67
D30V5, multiclass
D30V6, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            2                184
  CLUS_2            5                147
  CLUS_3            7                102
D30V7, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            5                192
  CLUS_2            4                175
  CLUS_3            6                 91
D30V8, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            6                 63
  CLUS_2            4                210
  CLUS_3            5                185
D30V9, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            4                111
  CLUS_2            5                186
  CLUS_3            7                162
D30V10, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            4                 31
  CLUS_2            4                156
  CLUS_3            8                272
D30V11, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            1                 49
  CLUS_2            0                 89
  CLUS_3            2                 72
D30V12, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            2                 55
  CLUS_2            0                 92
  CLUS_3            1                 63

Clustering(31) Variable = 17q gain
D31V1, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            0                 33
  CLUS_2            1                 23
  CLUS_3            3                 10
D31V2, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            3                 11
  CLUS_2            0                 32
  CLUS_3            1                 23
D31V3, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           12                152
  CLUS_2            3                213
  CLUS_3            7                117
D31V4, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            2                 97
  CLUS_2            5                114
  CLUS_3            6                 65
D31V5, multiclass
D31V6, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            4                182
  CLUS_2            7                145
  CLUS_3            9                100
D31V7, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            6                191
  CLUS_2            8                171
  CLUS_3            7                 90
D31V8, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            8                 61
  CLUS_2            5                209
  CLUS_3            8                182
D31V9, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            7                108
  CLUS_2            6                185
  CLUS_3            9                160
D31V10, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            5                 30
  CLUS_2            8                152
  CLUS_3            9                271
D31V11, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            1                 49
  CLUS_2            0                 89
  CLUS_3            4                 70
D31V12, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            3                 54
  CLUS_2            0                 92
  CLUS_3            2                 62

Clustering(32) Variable = 18p gain
D32V1, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            0                 33
  CLUS_2            3                 21
  CLUS_3            0                 13
D32V2, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            0                 32
  CLUS_3            3                 21
D32V3, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            7                157
  CLUS_2            5                211
  CLUS_3            6                118
D32V4, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            1                 98
  CLUS_2            7                112
  CLUS_3            2                 69
D32V5, multiclass
D32V6, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1           10                176
  CLUS_2            5                147
  CLUS_3            1                108
D32V7, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            4                193
  CLUS_2            6                173
  CLUS_3            7                 90
D32V8, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            4                 65
  CLUS_2            8                206
  CLUS_3            5                185
D32V9, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            5                110
  CLUS_2            7                184
  CLUS_3            6                163
D32V10, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            2                 33
  CLUS_2            5                155
  CLUS_3           11                269
D32V11, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            2                 48
  CLUS_2            5                 84
  CLUS_3            1                 73
D32V12, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            1                 56
  CLUS_2            6                 86
  CLUS_3            1                 63

Clustering(33) Variable = 18q gain
D33V1, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            0                 33
  CLUS_2            3                 21
  CLUS_3            0                 13
D33V2, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            0                 32
  CLUS_3            3                 21
D33V3, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            7                157
  CLUS_2            5                211
  CLUS_3            6                118
D33V4, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            1                 98
  CLUS_2            7                112
  CLUS_3            2                 69
D33V5, multiclass
D33V6, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1           10                176
  CLUS_2            5                147
  CLUS_3            1                108
D33V7, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            4                193
  CLUS_2            6                173
  CLUS_3            7                 90
D33V8, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            4                 65
  CLUS_2            8                206
  CLUS_3            5                185
D33V9, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            5                110
  CLUS_2            7                184
  CLUS_3            6                163
D33V10, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            2                 33
  CLUS_2            5                155
  CLUS_3           11                269
D33V11, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            2                 48
  CLUS_2            5                 84
  CLUS_3            1                 73
D33V12, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            1                 56
  CLUS_2            6                 86
  CLUS_3            1                 63

Clustering(34) Variable = 19p gain
D34V1, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            0                 33
  CLUS_2            2                 22
  CLUS_3            1                 12
D34V2, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            1                 13
  CLUS_2            0                 32
  CLUS_3            2                 22
D34V3, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1           16                148
  CLUS_2            1                215
  CLUS_3            8                116
D34V4, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            8                 91
  CLUS_2            4                115
  CLUS_3            3                 68
D34V5, multiclass
D34V6, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            7                179
  CLUS_2            8                144
  CLUS_3            8                101
D34V7, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            4                193
  CLUS_2           12                167
  CLUS_3            7                 90
D34V8, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            4                 65
  CLUS_2            4                210
  CLUS_3           15                175
D34V9, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            4                111
  CLUS_2            6                185
  CLUS_3           15                154
D34V10, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            4                 31
  CLUS_2           11                149
  CLUS_3           10                270
D34V11, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            4                 46
  CLUS_2            1                 88
  CLUS_3            8                 66
D34V12, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            5                 52
  CLUS_2            3                 89
  CLUS_3            5                 59

Clustering(35) Variable = 19q gain
D35V1, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            0                 33
  CLUS_2            2                 22
  CLUS_3            2                 11
D35V2, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            2                 12
  CLUS_2            0                 32
  CLUS_3            2                 22
D35V3, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1           19                145
  CLUS_2            1                215
  CLUS_3            8                116
D35V4, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            9                 90
  CLUS_2            4                115
  CLUS_3            3                 68
D35V5, multiclass
D35V6, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            7                179
  CLUS_2            9                143
  CLUS_3           10                 99
D35V7, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            4                193
  CLUS_2           14                165
  CLUS_3            7                 90
D35V8, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            4                 65
  CLUS_2            4                210
  CLUS_3           17                173
D35V9, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            4                111
  CLUS_2            6                185
  CLUS_3           17                152
D35V10, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            4                 31
  CLUS_2           12                148
  CLUS_3           11                269
D35V11, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            4                 46
  CLUS_2            1                 88
  CLUS_3            9                 65
D35V12, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            6                 51
  CLUS_2            3                 89
  CLUS_3            5                 59

Clustering(36) Variable = 20p gain
D36V1, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            1                 32
  CLUS_2            3                 21
  CLUS_3            3                 10
D36V2, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            3                 11
  CLUS_2            1                 31
  CLUS_3            3                 21
D36V3, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           44                120
  CLUS_2            3                213
  CLUS_3           20                104
D36V4, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           23                 76
  CLUS_2            8                111
  CLUS_3            9                 62
D36V5, multiclass
D36V6, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           14                172
  CLUS_2           22                130
  CLUS_3           25                 84
D36V7, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           12                185
  CLUS_2           42                137
  CLUS_3           10                 87
D36V8, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            8                 61
  CLUS_2           13                201
  CLUS_3           43                147
D36V9, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           11                104
  CLUS_2           13                178
  CLUS_3           42                127
D36V10, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            8                 27
  CLUS_2           28                132
  CLUS_3           30                250
D36V11, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            3                 47
  CLUS_2            1                 88
  CLUS_3           22                 52
D36V12, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           16                 41
  CLUS_2            3                 89
  CLUS_3            7                 57

Clustering(37) Variable = 20q gain
D37V1, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            1                 32
  CLUS_2            4                 20
  CLUS_3            3                 10
D37V2, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            3                 11
  CLUS_2            1                 31
  CLUS_3            4                 20
D37V3, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           47                117
  CLUS_2            3                213
  CLUS_3           19                105
D37V4, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           23                 76
  CLUS_2            8                111
  CLUS_3            9                 62
D37V5, multiclass
D37V6, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           14                172
  CLUS_2           24                128
  CLUS_3           25                 84
D37V7, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           12                185
  CLUS_2           45                134
  CLUS_3            9                 88
D37V8, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            8                 61
  CLUS_2           13                201
  CLUS_3           45                145
D37V9, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           10                105
  CLUS_2           13                178
  CLUS_3           45                124
D37V10, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            8                 27
  CLUS_2           29                131
  CLUS_3           31                249
D37V11, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            3                 47
  CLUS_2            1                 88
  CLUS_3           24                 50
D37V12, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           18                 39
  CLUS_2            3                 89
  CLUS_3            7                 57

Clustering(38) Variable = 21q gain
D38V1, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            2                 31
  CLUS_2            2                 22
  CLUS_3            0                 13
D38V2, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            2                 30
  CLUS_3            2                 22
D38V3, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           22                142
  CLUS_2            9                207
  CLUS_3            4                120
D38V4, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           12                 87
  CLUS_2            6                113
  CLUS_3            3                 68
D38V5, multiclass
D38V6, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           11                175
  CLUS_2           11                141
  CLUS_3            8                101
D38V7, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            8                189
  CLUS_2           18                161
  CLUS_3            6                 91
D38V8, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            3                 66
  CLUS_2           10                204
  CLUS_3           19                171
D38V9, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            7                108
  CLUS_2           10                181
  CLUS_3           16                153
D38V10, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            2                 33
  CLUS_2           13                147
  CLUS_3           18                262
D38V11, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            3                 47
  CLUS_2            1                 88
  CLUS_3            7                 67
D38V12, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            8                 49
  CLUS_2            2                 90
  CLUS_3            1                 63

Clustering(39) Variable = 22q gain
D39V1, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            1                 32
  CLUS_2            2                 22
  CLUS_3            0                 13
D39V2, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            0                 32
  CLUS_3            3                 21
D39V3, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1           16                148
  CLUS_2            4                212
  CLUS_3            5                119
D39V4, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            7                 92
  CLUS_2            7                112
  CLUS_3            0                 71
D39V5, multiclass
D39V6, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1           12                174
  CLUS_2            4                148
  CLUS_3            7                102
D39V7, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            9                188
  CLUS_2            9                170
  CLUS_3            6                 91
D39V8, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            3                 66
  CLUS_2           10                204
  CLUS_3           11                179
D39V9, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            6                109
  CLUS_2            9                182
  CLUS_3            9                160
D39V10, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            2                 33
  CLUS_2            7                153
  CLUS_3           15                265
D39V11, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            1                 49
  CLUS_2            1                 88
  CLUS_3            3                 71
D39V12, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            1                 56
  CLUS_2            3                 89
  CLUS_3            1                 63

Clustering(40) Variable = Xq gain
D40V1, multiclass
[1] "Remove cluster labels:" "XQ GAIN CNV"           
clus
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                2                68 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A3-3374        TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A3-3383        TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AK-3443        TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3455 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D40V2, multiclass
[1] "Remove cluster labels:" "XQ GAIN CNV"           
clus
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                2                68 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A3-3374        TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A3-3383        TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AK-3443        TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3455 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D40V3, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           4               160
  CLUS_2           2               214
  CLUS_3           3               121
D40V4, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           1                98
  CLUS_2           3               116
  CLUS_3           1                70
D40V5, multiclass
D40V6, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           2               184
  CLUS_2           1               151
  CLUS_3           3               106
D40V7, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           1               196
  CLUS_2           4               175
  CLUS_3           4                93
D40V8, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           3                66
  CLUS_2           2               212
  CLUS_3           4               186
D40V9, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           1               114
  CLUS_2           2               189
  CLUS_3           6               163
D40V10, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           2                33
  CLUS_2           3               157
  CLUS_3           4               276
D40V11, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           1                49
  CLUS_2           2                87
  CLUS_3           2                72
D40V12, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           2                55
  CLUS_2           2                90
  CLUS_3           1                63

Clustering(41) Variable = 1p loss
D41V1, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           2                31
  CLUS_2           2                22
  CLUS_3           7                 6
D41V2, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           8                 6
  CLUS_2           2                30
  CLUS_3           1                23
D41V3, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1          10               154
  CLUS_2           4               212
  CLUS_3          18               106
D41V4, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           3                96
  CLUS_2           5               114
  CLUS_3           5                66
D41V5, multiclass
D41V6, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1          10               176
  CLUS_2           2               150
  CLUS_3          14                95
D41V7, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           9               188
  CLUS_2           8               171
  CLUS_3          13                84
D41V8, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1          15                54
  CLUS_2           9               205
  CLUS_3           6               184
D41V9, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           5               110
  CLUS_2           8               183
  CLUS_3          19               150
D41V10, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1          15                20
  CLUS_2           4               156
  CLUS_3          13               267
D41V11, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           3                47
  CLUS_2           3                86
  CLUS_3           5                69
D41V12, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           7                50
  CLUS_2           2                90
  CLUS_3           2                62

Clustering(42) Variable = 1q loss
D42V1, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           2                31
  CLUS_2           1                23
  CLUS_3           5                 8
D42V2, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           5                 9
  CLUS_2           2                30
  CLUS_3           1                23
D42V3, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           4               160
  CLUS_2           1               215
  CLUS_3          15               109
D42V4, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           3                96
  CLUS_2           3               116
  CLUS_3           2                69
D42V5, multiclass
D42V6, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           5               181
  CLUS_2           1               151
  CLUS_3          10                99
D42V7, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           5               192
  CLUS_2           2               177
  CLUS_3          13                84
D42V8, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1          12                57
  CLUS_2           5               209
  CLUS_3           3               187
D42V9, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           3               112
  CLUS_2           5               186
  CLUS_3          12               157
D42V10, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1          12                23
  CLUS_2           3               157
  CLUS_3           5               275
D42V11, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           3                47
  CLUS_2           1                88
  CLUS_3           3                71
D42V12, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           5                52
  CLUS_2           0                92
  CLUS_3           2                62

Clustering(43) Variable = 2p loss
D43V1, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           0                33
  CLUS_2           1                23
  CLUS_3           5                 8
D43V2, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           5                 9
  CLUS_2           0                32
  CLUS_3           1                23
D43V3, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           0               164
  CLUS_2           0               216
  CLUS_3          10               114
D43V4, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           0                99
  CLUS_2           2               117
  CLUS_3           1                70
D43V5, multiclass
D43V6, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           0               186
  CLUS_2           0               152
  CLUS_3           6               103
D43V7, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           0               197
  CLUS_2           0               179
  CLUS_3           9                88
D43V8, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           9                60
  CLUS_2           0               214
  CLUS_3           0               190
D43V9, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           1               114
  CLUS_2           0               191
  CLUS_3           9               160
D43V10, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1          10                25
  CLUS_2           0               160
  CLUS_3           0               280
D43V11, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           1                49
  CLUS_2           1                88
  CLUS_3           1                73
D43V12, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           3                54
  CLUS_2           0                92
  CLUS_3           0                64

Clustering(44) Variable = 2q loss
D44V1, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           0                33
  CLUS_2           1                23
  CLUS_3           5                 8
D44V2, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           5                 9
  CLUS_2           0                32
  CLUS_3           1                23
D44V3, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1               163
  CLUS_2           0               216
  CLUS_3          10               114
D44V4, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1                98
  CLUS_2           2               117
  CLUS_3           1                70
D44V5, multiclass
D44V6, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           0               186
  CLUS_2           0               152
  CLUS_3           7               102
D44V7, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           0               197
  CLUS_2           0               179
  CLUS_3          10                87
D44V8, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           9                60
  CLUS_2           0               214
  CLUS_3           1               189
D44V9, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1               114
  CLUS_2           0               191
  CLUS_3          10               159
D44V10, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1          10                25
  CLUS_2           1               159
  CLUS_3           0               280
D44V11, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1                49
  CLUS_2           1                88
  CLUS_3           1                73
D44V12, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           3                54
  CLUS_2           0                92
  CLUS_3           0                64

Clustering(45) Variable = 3p loss
D45V1, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          21                12
  CLUS_2          11                13
  CLUS_3           2                11
D45V2, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           2                12
  CLUS_2          20                12
  CLUS_3          12                12
D45V3, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1         118                46
  CLUS_2         174                42
  CLUS_3          19               105
D45V4, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          65                34
  CLUS_2          91                28
  CLUS_3          29                42
D45V5, multiclass
D45V6, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1         130                56
  CLUS_2         101                51
  CLUS_3          47                62
D45V7, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1         154                43
  CLUS_2          96                83
  CLUS_3          38                59
D45V8, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          23                46
  CLUS_2         160                54
  CLUS_3         105                85
D45V9, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          63                52
  CLUS_2         140                51
  CLUS_3          88                81
D45V10, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           7                28
  CLUS_2          74                86
  CLUS_3         210                70
D45V11, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          24                26
  CLUS_2          63                26
  CLUS_3          42                32
D45V12, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          35                22
  CLUS_2          69                23
  CLUS_3          25                39

Clustering(46) Variable = 3q loss
D46V1, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           5                28
  CLUS_2           2                22
  CLUS_3           1                12
D46V2, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           1                13
  CLUS_2           5                27
  CLUS_3           2                22
D46V3, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1          33               131
  CLUS_2          38               178
  CLUS_3           3               121
D46V4, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1          18                81
  CLUS_2          18               101
  CLUS_3           6                65
D46V5, multiclass
D46V6, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1          35               151
  CLUS_2          27               125
  CLUS_3           7               102
D46V7, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1          25               172
  CLUS_2          25               154
  CLUS_3          17                80
D46V8, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1          10                59
  CLUS_2          28               186
  CLUS_3          29               161
D46V9, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1          15               100
  CLUS_2          30               161
  CLUS_3          26               143
D46V10, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           0                35
  CLUS_2          22               138
  CLUS_3          49               231
D46V11, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           7                43
  CLUS_2           7                82
  CLUS_3          13                61
D46V12, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1          11                46
  CLUS_2           9                83
  CLUS_3           7                57

Clustering(47) Variable = 4p loss
D47V1, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           3                30
  CLUS_2           0                24
  CLUS_3           0                13
D47V2, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           0                14
  CLUS_2           3                29
  CLUS_3           0                24
D47V3, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1          20               144
  CLUS_2           7               209
  CLUS_3           8               116
D47V4, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1          13                86
  CLUS_2           7               112
  CLUS_3           4                67
D47V5, multiclass
D47V6, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1          14               172
  CLUS_2          11               141
  CLUS_3           9               100
D47V7, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1          16               181
  CLUS_2          14               165
  CLUS_3           2                95
D47V8, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           2                67
  CLUS_2          17               197
  CLUS_3          13               177
D47V9, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           7               108
  CLUS_2          17               174
  CLUS_3          10               159
D47V10, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           1                34
  CLUS_2          12               148
  CLUS_3          21               259
D47V11, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           3                47
  CLUS_2           4                85
  CLUS_3           7                67
D47V12, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           5                52
  CLUS_2           4                88
  CLUS_3           5                59

Clustering(48) Variable = 4q loss
D48V1, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           2                31
  CLUS_2           1                23
  CLUS_3           0                13
D48V2, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           0                14
  CLUS_2           2                30
  CLUS_3           1                23
D48V3, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1          20               144
  CLUS_2           3               213
  CLUS_3           5               119
D48V4, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1          11                88
  CLUS_2           5               114
  CLUS_3           3                68
D48V5, multiclass
D48V6, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1          11               175
  CLUS_2           7               145
  CLUS_3          10                99
D48V7, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1          11               186
  CLUS_2          13               166
  CLUS_3           1                96
D48V8, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           0                69
  CLUS_2          12               202
  CLUS_3          13               177
D48V9, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           6               109
  CLUS_2          12               179
  CLUS_3          10               159
D48V10, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           0                35
  CLUS_2          11               149
  CLUS_3          17               263
D48V11, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           3                47
  CLUS_2           2                87
  CLUS_3           6                68
D48V12, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           4                53
  CLUS_2           2                90
  CLUS_3           5                59

Clustering(49) Variable = 6p loss
D49V1, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           2                31
  CLUS_2           6                18
  CLUS_3           5                 8
D49V2, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           5                 9
  CLUS_2           1                31
  CLUS_3           7                17
D49V3, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1          40               124
  CLUS_2           5               211
  CLUS_3          14               110
D49V4, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1          18                81
  CLUS_2           5               114
  CLUS_3           6                65
D49V5, multiclass
D49V6, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           8               178
  CLUS_2          19               133
  CLUS_3          25                84
D49V7, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1          11               186
  CLUS_2          32               147
  CLUS_3          10                87
D49V8, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           9                60
  CLUS_2          12               202
  CLUS_3          32               158
D49V9, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           3               112
  CLUS_2          12               179
  CLUS_3          41               128
D49V10, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1          12                23
  CLUS_2          19               141
  CLUS_3          25               255
D49V11, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           1                49
  CLUS_2           5                84
  CLUS_3          15                59
D49V12, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1          14                43
  CLUS_2           3                89
  CLUS_3           4                60

Clustering(50) Variable = 6q loss
D50V1, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           4                29
  CLUS_2           7                17
  CLUS_3           6                 7
D50V2, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           6                 8
  CLUS_2           3                29
  CLUS_3           8                16
D50V3, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          53               111
  CLUS_2          18               198
  CLUS_3          14               110
D50V4, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          21                78
  CLUS_2          14               105
  CLUS_3           9                62
D50V5, multiclass
D50V6, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          18               168
  CLUS_2          29               123
  CLUS_3          28                81
D50V7, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          29               168
  CLUS_2          36               143
  CLUS_3          12                85
D50V8, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          12                57
  CLUS_2          30               184
  CLUS_3          35               155
D50V9, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           8               107
  CLUS_2          26               165
  CLUS_3          46               123
D50V10, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          14                21
  CLUS_2          23               137
  CLUS_3          43               237
D50V11, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           4                46
  CLUS_2          13                76
  CLUS_3          19                55
D50V12, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          19                38
  CLUS_2          10                82
  CLUS_3           7                57

Clustering(51) Variable = 8p loss
D51V1, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           5                28
  CLUS_2           5                19
  CLUS_3           3                10
D51V2, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           3                11
  CLUS_2           5                27
  CLUS_3           5                19
D51V3, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          46               118
  CLUS_2          37               179
  CLUS_3          16               108
D51V4, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          21                78
  CLUS_2          22                97
  CLUS_3          11                60
D51V5, multiclass
D51V6, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          33               153
  CLUS_2          31               121
  CLUS_3          24                85
D51V7, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          42               155
  CLUS_2          38               141
  CLUS_3          12                85
D51V8, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          10                59
  CLUS_2          43               171
  CLUS_3          39               151
D51V9, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          18                97
  CLUS_2          37               154
  CLUS_3          42               127
D51V10, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           4                31
  CLUS_2          34               126
  CLUS_3          59               221
D51V11, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          11                39
  CLUS_2          14                75
  CLUS_3          17                57
D51V12, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          13                44
  CLUS_2          15                77
  CLUS_3          14                50

Clustering(52) Variable = 8q loss
D52V1, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           2                31
  CLUS_2           1                23
  CLUS_3           2                11
D52V2, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           2                12
  CLUS_2           2                30
  CLUS_3           1                23
D52V3, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1          14               150
  CLUS_2          17               199
  CLUS_3           9               115
D52V4, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           9                90
  CLUS_2          12               107
  CLUS_3           2                69
D52V5, multiclass
D52V6, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1          17               169
  CLUS_2          10               142
  CLUS_3           9               100
D52V7, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1          21               176
  CLUS_2          10               169
  CLUS_3           7                90
D52V8, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           5                64
  CLUS_2          24               190
  CLUS_3           9               181
D52V9, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           9               106
  CLUS_2          17               174
  CLUS_3          13               156
D52V10, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           4                31
  CLUS_2           9               151
  CLUS_3          26               254
D52V11, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           6                44
  CLUS_2           6                83
  CLUS_3           5                69
D52V12, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           4                53
  CLUS_2           5                87
  CLUS_3           8                56

Clustering(53) Variable = 9p loss
D53V1, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           4                29
  CLUS_2           6                18
  CLUS_3           1                12
D53V2, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           1                13
  CLUS_2           3                29
  CLUS_3           7                17
D53V3, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          77                87
  CLUS_2           3               213
  CLUS_3           9               115
D53V4, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          39                60
  CLUS_2           3               116
  CLUS_3          11                60
D53V5, multiclass
D53V6, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          22               164
  CLUS_2          33               119
  CLUS_3          27                82
D53V7, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          14               183
  CLUS_2          60               119
  CLUS_3           9                88
D53V8, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           5                64
  CLUS_2          15               199
  CLUS_3          63               127
D53V9, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          13               102
  CLUS_2          17               174
  CLUS_3          55               114
D53V10, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           7                28
  CLUS_2          35               125
  CLUS_3          43               237
D53V11, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           5                45
  CLUS_2           6                83
  CLUS_3          28                46
D53V12, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          23                34
  CLUS_2           9                83
  CLUS_3           7                57

Clustering(54) Variable = 9q loss
D54V1, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           4                29
  CLUS_2           6                18
  CLUS_3           1                12
D54V2, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           1                13
  CLUS_2           3                29
  CLUS_3           7                17
D54V3, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          81                83
  CLUS_2           4               212
  CLUS_3           9               115
D54V4, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          41                58
  CLUS_2           3               116
  CLUS_3          11                60
D54V5, multiclass
D54V6, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          24               162
  CLUS_2          36               116
  CLUS_3          27                82
D54V7, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          15               182
  CLUS_2          64               115
  CLUS_3           9                88
D54V8, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           5                64
  CLUS_2          15               199
  CLUS_3          68               122
D54V9, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          13               102
  CLUS_2          17               174
  CLUS_3          59               110
D54V10, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           7                28
  CLUS_2          37               123
  CLUS_3          45               235
D54V11, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           5                45
  CLUS_2           8                81
  CLUS_3          30                44
D54V12, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          24                33
  CLUS_2          11                81
  CLUS_3           8                56

Clustering(55) Variable = 10p loss
D55V1, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            1                 32
  CLUS_2            2                 22
  CLUS_3            4                  9
D55V2, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            4                 10
  CLUS_2            1                 31
  CLUS_3            2                 22
D55V3, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1           14                150
  CLUS_2            2                214
  CLUS_3           16                108
D55V4, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1           11                 88
  CLUS_2            6                113
  CLUS_3            3                 68
D55V5, multiclass
D55V6, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1           10                176
  CLUS_2            5                147
  CLUS_3           12                 97
D55V7, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            9                188
  CLUS_2            8                171
  CLUS_3           13                 84
D55V8, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1           10                 59
  CLUS_2           10                204
  CLUS_3           10                180
D55V9, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            9                106
  CLUS_2            8                183
  CLUS_3           15                154
D55V10, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            9                 26
  CLUS_2            9                151
  CLUS_3           14                266
D55V11, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            5                 45
  CLUS_2            3                 86
  CLUS_3            7                 67
D55V12, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            8                 49
  CLUS_2            3                 89
  CLUS_3            4                 60

Clustering(56) Variable = 10q loss
D56V1, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            2                 31
  CLUS_2            2                 22
  CLUS_3            4                  9
D56V2, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            4                 10
  CLUS_2            2                 30
  CLUS_3            2                 22
D56V3, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           22                142
  CLUS_2            9                207
  CLUS_3           17                107
D56V4, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           17                 82
  CLUS_2            9                110
  CLUS_3            3                 68
D56V5, multiclass
D56V6, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           17                169
  CLUS_2            8                144
  CLUS_3           18                 91
D56V7, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           15                182
  CLUS_2           15                164
  CLUS_3           15                 82
D56V8, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           11                 58
  CLUS_2           16                198
  CLUS_3           18                172
D56V9, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           10                105
  CLUS_2           16                175
  CLUS_3           22                147
D56V10, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            9                 26
  CLUS_2           14                146
  CLUS_3           25                255
D56V11, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            5                 45
  CLUS_2            7                 82
  CLUS_3           10                 64
D56V12, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           12                 45
  CLUS_2            6                 86
  CLUS_3            4                 60

Clustering(57) Variable = 11p loss
D57V1, multiclass
[1] "Remove cluster labels:" "11P LOSS CNV"          
clus
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3374         TCGA-A3-3378 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3380         TCGA-A3-3382         TCGA-A3-3383 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3427         TCGA-AK-3440 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AK-3443         TCGA-AK-3444         TCGA-AK-3447 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AK-3453         TCGA-AK-3455         TCGA-AK-3456 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
D57V2, multiclass
[1] "Remove cluster labels:" "11P LOSS CNV"          
clus
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3374         TCGA-A3-3378 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3380         TCGA-A3-3382         TCGA-A3-3383 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3427         TCGA-AK-3440 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AK-3443         TCGA-AK-3444         TCGA-AK-3447 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AK-3453         TCGA-AK-3455         TCGA-AK-3456 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
D57V3, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            4                160
  CLUS_2            0                216
  CLUS_3            1                123
D57V4, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            2                 97
  CLUS_2            1                118
  CLUS_3            0                 71
D57V5, multiclass
D57V6, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            0                186
  CLUS_2            1                151
  CLUS_3            3                106
D57V7, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            1                196
  CLUS_2            2                177
  CLUS_3            2                 95
D57V8, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            1                 68
  CLUS_2            1                213
  CLUS_3            3                187
D57V9, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            1                114
  CLUS_2            1                190
  CLUS_3            3                166
D57V10, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            1                 34
  CLUS_2            3                157
  CLUS_3            1                279
D57V11, multiclass
[1] "Remove cluster labels:" "11P LOSS CNV"          
clus
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 2                211 
        TCGA-A3-3317         TCGA-A3-3358         TCGA-A3-3387 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AK-3440         TCGA-AK-3458         TCGA-B0-4698 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-4700         TCGA-B0-4706         TCGA-B0-4710 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-4712         TCGA-B0-4810         TCGA-B0-4811 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-4815         TCGA-B0-4816         TCGA-B0-4818 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-4821         TCGA-B0-4833         TCGA-B0-4834 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-4836         TCGA-B0-4837         TCGA-B0-4852 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-5075         TCGA-B0-5080         TCGA-B0-5085 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-5088         TCGA-B0-5399         TCGA-B0-5400 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-5402         TCGA-B0-5690         TCGA-B0-5691 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-5692         TCGA-B0-5693         TCGA-B0-5694 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-5695         TCGA-B0-5696         TCGA-B0-5697 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-5698         TCGA-B0-5699         TCGA-B0-5701 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-5702         TCGA-B0-5703         TCGA-B0-5705 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-5706         TCGA-B0-5709         TCGA-B0-5710 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-5711         TCGA-B0-5712         TCGA-B0-5713 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-5812         TCGA-B2-5633         TCGA-B2-5635 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B2-5639         TCGA-B2-5641         TCGA-B4-5377 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B4-5378         TCGA-B4-5832         TCGA-B4-5834 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5838 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B4-5843         TCGA-B4-5844         TCGA-B8-4146 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B8-4153         TCGA-B8-4621         TCGA-B8-5545 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B8-5546         TCGA-B8-5549         TCGA-B8-5550 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B8-5551         TCGA-B8-5552         TCGA-B8-5553 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4173         TCGA-BP-4331         TCGA-BP-4340 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4759         TCGA-BP-4761         TCGA-BP-4770 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4771         TCGA-BP-4787         TCGA-BP-4789 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4790         TCGA-BP-4797         TCGA-BP-4804 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4807         TCGA-BP-4959         TCGA-BP-4960 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4961         TCGA-BP-4965         TCGA-BP-4967 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4968         TCGA-BP-4969         TCGA-BP-4970 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4971         TCGA-BP-4973         TCGA-BP-4974 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4975         TCGA-BP-4976         TCGA-BP-4977 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4981         TCGA-BP-4982         TCGA-BP-4985 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4986         TCGA-BP-4987         TCGA-BP-4988 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4989         TCGA-BP-4992         TCGA-BP-4994 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4995         TCGA-BP-4998         TCGA-BP-5000 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-5001         TCGA-BP-5007         TCGA-BP-5008 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-5009         TCGA-CJ-4635         TCGA-CJ-4870 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-4875         TCGA-CJ-4876         TCGA-CJ-4878 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-4881         TCGA-CJ-4887         TCGA-CJ-4888 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-4889         TCGA-CJ-4890         TCGA-CJ-4891 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-4895         TCGA-CJ-4899         TCGA-CJ-4900 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-5671         TCGA-CJ-5672         TCGA-CJ-5675 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-5676         TCGA-CJ-5677         TCGA-CJ-5678 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-5679         TCGA-CJ-5680         TCGA-CJ-5681 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-5682         TCGA-CJ-5683         TCGA-CJ-5684 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-5686         TCGA-CJ-5689         TCGA-CJ-6027 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-6028         TCGA-CJ-6030         TCGA-CJ-6031 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-6032         TCGA-CJ-6033         TCGA-CW-5580 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CW-5581         TCGA-CW-5583         TCGA-CW-5584 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CW-5585         TCGA-CW-5587         TCGA-CW-5588 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CW-5589         TCGA-CW-5591         TCGA-CW-6087 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CW-6088         TCGA-CW-6090         TCGA-CW-6093 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CW-6097         TCGA-CZ-4854         TCGA-CZ-4857 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CZ-4858         TCGA-CZ-4860         TCGA-CZ-4863 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CZ-4864         TCGA-CZ-4865         TCGA-CZ-4866 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CZ-5451         TCGA-CZ-5452         TCGA-CZ-5453 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CZ-5454         TCGA-CZ-5455         TCGA-CZ-5456 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CZ-5457         TCGA-CZ-5458         TCGA-CZ-5459 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CZ-5460         TCGA-CZ-5461         TCGA-CZ-5462 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CZ-5463         TCGA-CZ-5464         TCGA-CZ-5465 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CZ-5466         TCGA-CZ-5467         TCGA-CZ-5468 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CZ-5469         TCGA-CZ-5470         TCGA-CZ-5982 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CZ-5984         TCGA-CZ-5985         TCGA-CZ-5986 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CZ-5987         TCGA-CZ-5988         TCGA-CZ-5989 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DV-5565         TCGA-DV-5566         TCGA-DV-5567 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DV-5568         TCGA-DV-5569         TCGA-DV-5573 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DV-5574         TCGA-DV-5575         TCGA-DV-5576 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EU-5904         TCGA-EU-5905         TCGA-EU-5906 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EU-5907 
"11P LOSS WILD-TYPE" 
D57V12, multiclass
[1] "Remove cluster labels:" "11P LOSS CNV"          
clus
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 2                211 
        TCGA-A3-3317         TCGA-A3-3358         TCGA-A3-3387 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AK-3440         TCGA-AK-3458         TCGA-B0-4698 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-4700         TCGA-B0-4706         TCGA-B0-4710 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-4712         TCGA-B0-4810         TCGA-B0-4811 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-4815         TCGA-B0-4816         TCGA-B0-4818 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-4821         TCGA-B0-4833         TCGA-B0-4834 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-4836         TCGA-B0-4837         TCGA-B0-4852 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-5075         TCGA-B0-5080         TCGA-B0-5085 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-5088         TCGA-B0-5399         TCGA-B0-5400 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-5402         TCGA-B0-5690         TCGA-B0-5691 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-5692         TCGA-B0-5693         TCGA-B0-5694 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-5695         TCGA-B0-5696         TCGA-B0-5697 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-5698         TCGA-B0-5699         TCGA-B0-5701 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-5702         TCGA-B0-5703         TCGA-B0-5705 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-5706         TCGA-B0-5709         TCGA-B0-5710 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-5711         TCGA-B0-5712         TCGA-B0-5713 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B0-5812         TCGA-B2-5633         TCGA-B2-5635 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B2-5639         TCGA-B2-5641         TCGA-B4-5377 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B4-5378         TCGA-B4-5832         TCGA-B4-5834 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5838 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B4-5843         TCGA-B4-5844         TCGA-B8-4146 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B8-4153         TCGA-B8-4621         TCGA-B8-5545 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B8-5546         TCGA-B8-5549         TCGA-B8-5550 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B8-5551         TCGA-B8-5552         TCGA-B8-5553 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4173         TCGA-BP-4331         TCGA-BP-4340 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4759         TCGA-BP-4761         TCGA-BP-4770 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4771         TCGA-BP-4787         TCGA-BP-4789 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4790         TCGA-BP-4797         TCGA-BP-4804 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4807         TCGA-BP-4959         TCGA-BP-4960 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4961         TCGA-BP-4965         TCGA-BP-4967 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4968         TCGA-BP-4969         TCGA-BP-4970 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4971         TCGA-BP-4973         TCGA-BP-4974 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4975         TCGA-BP-4976         TCGA-BP-4977 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4981         TCGA-BP-4982         TCGA-BP-4985 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4986         TCGA-BP-4987         TCGA-BP-4988 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4989         TCGA-BP-4992         TCGA-BP-4994 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4995         TCGA-BP-4998         TCGA-BP-5000 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-5001         TCGA-BP-5007         TCGA-BP-5008 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-5009         TCGA-CJ-4635         TCGA-CJ-4870 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-4875         TCGA-CJ-4876         TCGA-CJ-4878 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-4881         TCGA-CJ-4887         TCGA-CJ-4888 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-4889         TCGA-CJ-4890         TCGA-CJ-4891 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-4895         TCGA-CJ-4899         TCGA-CJ-4900 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-5671         TCGA-CJ-5672         TCGA-CJ-5675 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-5676         TCGA-CJ-5677         TCGA-CJ-5678 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-5679         TCGA-CJ-5680         TCGA-CJ-5681 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-5682         TCGA-CJ-5683         TCGA-CJ-5684 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-5686         TCGA-CJ-5689         TCGA-CJ-6027 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-6028         TCGA-CJ-6030         TCGA-CJ-6031 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-6032         TCGA-CJ-6033         TCGA-CW-5580 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CW-5581         TCGA-CW-5583         TCGA-CW-5584 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CW-5585         TCGA-CW-5587         TCGA-CW-5588 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CW-5589         TCGA-CW-5591         TCGA-CW-6087 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CW-6088         TCGA-CW-6090         TCGA-CW-6093 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CW-6097         TCGA-CZ-4854         TCGA-CZ-4857 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CZ-4858         TCGA-CZ-4860         TCGA-CZ-4863 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CZ-4864         TCGA-CZ-4865         TCGA-CZ-4866 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CZ-5451         TCGA-CZ-5452         TCGA-CZ-5453 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CZ-5454         TCGA-CZ-5455         TCGA-CZ-5456 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CZ-5457         TCGA-CZ-5458         TCGA-CZ-5459 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CZ-5460         TCGA-CZ-5461         TCGA-CZ-5462 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CZ-5463         TCGA-CZ-5464         TCGA-CZ-5465 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CZ-5466         TCGA-CZ-5467         TCGA-CZ-5468 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CZ-5469         TCGA-CZ-5470         TCGA-CZ-5982 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CZ-5984         TCGA-CZ-5985         TCGA-CZ-5986 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CZ-5987         TCGA-CZ-5988         TCGA-CZ-5989 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DV-5565         TCGA-DV-5566         TCGA-DV-5567 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DV-5568         TCGA-DV-5569         TCGA-DV-5573 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DV-5574         TCGA-DV-5575         TCGA-DV-5576 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EU-5904         TCGA-EU-5905         TCGA-EU-5906 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EU-5907 
"11P LOSS WILD-TYPE" 

Clustering(58) Variable = 11q loss
D58V1, multiclass
[1] "Remove cluster labels:" "11Q LOSS CNV"          
clus
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3374         TCGA-A3-3378 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3380         TCGA-A3-3382         TCGA-A3-3383 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3427         TCGA-AK-3440 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AK-3443         TCGA-AK-3444         TCGA-AK-3447 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AK-3453         TCGA-AK-3455         TCGA-AK-3456 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
D58V2, multiclass
[1] "Remove cluster labels:" "11Q LOSS CNV"          
clus
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3374         TCGA-A3-3378 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3380         TCGA-A3-3382         TCGA-A3-3383 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3427         TCGA-AK-3440 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AK-3443         TCGA-AK-3444         TCGA-AK-3447 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AK-3453         TCGA-AK-3455         TCGA-AK-3456 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
D58V3, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            6                158
  CLUS_2            0                216
  CLUS_3            1                123
D58V4, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            2                 97
  CLUS_2            1                118
  CLUS_3            1                 70
D58V5, multiclass
D58V6, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            1                185
  CLUS_2            1                151
  CLUS_3            3                106
D58V7, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            1                196
  CLUS_2            3                176
  CLUS_3            2                 95
D58V8, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            1                 68
  CLUS_2            1                213
  CLUS_3            4                186
D58V9, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            2                113
  CLUS_2            1                190
  CLUS_3            4                165
D58V10, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            1                 34
  CLUS_2            5                155
  CLUS_3            1                279
D58V11, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            1                 49
  CLUS_2            0                 89
  CLUS_3            2                 72
D58V12, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            2                 55
  CLUS_2            0                 92
  CLUS_3            1                 63

Clustering(59) Variable = 13q loss
D59V1, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            0                 33
  CLUS_2            4                 20
  CLUS_3            2                 11
D59V2, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            2                 12
  CLUS_2            0                 32
  CLUS_3            4                 20
D59V3, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           20                144
  CLUS_2            2                214
  CLUS_3            9                115
D59V4, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            9                 90
  CLUS_2            3                116
  CLUS_3            5                 66
D59V5, multiclass
D59V6, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            4                182
  CLUS_2           10                142
  CLUS_3           14                 95
D59V7, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            4                193
  CLUS_2           17                162
  CLUS_3            9                 88
D59V8, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            7                 62
  CLUS_2            4                210
  CLUS_3           19                171
D59V9, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            7                108
  CLUS_2            4                187
  CLUS_3           20                149
D59V10, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            7                 28
  CLUS_2           15                145
  CLUS_3            9                271
D59V11, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            3                 47
  CLUS_2            2                 87
  CLUS_3            9                 65
D59V12, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            9                 48
  CLUS_2            1                 91
  CLUS_3            4                 60

Clustering(60) Variable = 14q loss
D60V1, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            7                 26
  CLUS_2           15                  9
  CLUS_3            2                 11
D60V2, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            3                 11
  CLUS_2            6                 26
  CLUS_3           15                  9
D60V3, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           90                 74
  CLUS_2           46                170
  CLUS_3           26                 98
D60V4, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           44                 55
  CLUS_2           21                 98
  CLUS_3           25                 46
D60V5, multiclass
D60V6, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           37                149
  CLUS_2           73                 79
  CLUS_3           39                 70
D60V7, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           54                143
  CLUS_2           88                 91
  CLUS_3           11                 86
D60V8, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            8                 61
  CLUS_2           60                154
  CLUS_3           85                105
D60V9, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           25                 90
  CLUS_2           50                141
  CLUS_3           79                 90
D60V10, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           14                 21
  CLUS_2           48                112
  CLUS_3           92                188
D60V11, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           15                 35
  CLUS_2           27                 62
  CLUS_3           36                 38
D60V12, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           30                 27
  CLUS_2           30                 62
  CLUS_3           18                 46

Clustering(61) Variable = 15q loss
D61V1, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            1                 32
  CLUS_2            2                 22
  CLUS_3            0                 13
D61V2, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            1                 31
  CLUS_3            2                 22
D61V3, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            9                155
  CLUS_2            1                215
  CLUS_3            2                122
D61V4, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            3                 96
  CLUS_2            1                118
  CLUS_3            1                 70
D61V5, multiclass
D61V6, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            4                182
  CLUS_2            4                148
  CLUS_3            4                105
D61V7, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            4                193
  CLUS_2            8                171
  CLUS_3            0                 97
D61V8, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            0                 69
  CLUS_2            4                210
  CLUS_3            8                182
D61V9, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            1                114
  CLUS_2            4                187
  CLUS_3            7                162
D61V10, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            1                 34
  CLUS_2            4                156
  CLUS_3            7                273
D61V11, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            1                 49
  CLUS_2            0                 89
  CLUS_3            4                 70
D61V12, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            3                 54
  CLUS_2            0                 92
  CLUS_3            2                 62

Clustering(62) Variable = 16q loss
D62V1, multiclass
[1] "Remove cluster labels:" "16Q LOSS CNV"          
clus
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 1                 69 
        TCGA-A3-3307         TCGA-A3-3308         TCGA-A3-3311 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3313         TCGA-A3-3316         TCGA-A3-3317 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3319         TCGA-A3-3320         TCGA-A3-3322 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3323         TCGA-A3-3324         TCGA-A3-3325 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3326         TCGA-A3-3331         TCGA-A3-3335 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3336         TCGA-A3-3343         TCGA-A3-3346 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3347         TCGA-A3-3349         TCGA-A3-3351 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3352         TCGA-A3-3359         TCGA-A3-3362 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3363         TCGA-A3-3365         TCGA-A3-3372 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3374         TCGA-A3-3378         TCGA-A3-3380 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3382         TCGA-A3-3383         TCGA-AK-3426 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AK-3427         TCGA-AK-3440         TCGA-AK-3443 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AK-3444         TCGA-AK-3447         TCGA-AK-3453 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AK-3455         TCGA-AK-3456         TCGA-AK-3465 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D62V2, multiclass
[1] "Remove cluster labels:" "16Q LOSS CNV"          
clus
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 1                 69 
        TCGA-A3-3307         TCGA-A3-3308         TCGA-A3-3311 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3313         TCGA-A3-3316         TCGA-A3-3317 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3319         TCGA-A3-3320         TCGA-A3-3322 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3323         TCGA-A3-3324         TCGA-A3-3325 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3326         TCGA-A3-3331         TCGA-A3-3335 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3336         TCGA-A3-3343         TCGA-A3-3346 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3347         TCGA-A3-3349         TCGA-A3-3351 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3352         TCGA-A3-3359         TCGA-A3-3362 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3363         TCGA-A3-3365         TCGA-A3-3372 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3374         TCGA-A3-3378         TCGA-A3-3380 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3382         TCGA-A3-3383         TCGA-AK-3426 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AK-3427         TCGA-AK-3440         TCGA-AK-3443 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AK-3444         TCGA-AK-3447         TCGA-AK-3453 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AK-3455         TCGA-AK-3456         TCGA-AK-3465 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D62V3, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            4                160
  CLUS_2            1                215
  CLUS_3            1                123
D62V4, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            2                 97
  CLUS_2            0                119
  CLUS_3            1                 70
D62V5, multiclass
D62V6, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            1                185
  CLUS_2            3                149
  CLUS_3            1                108
D62V7, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            2                195
  CLUS_2            2                177
  CLUS_3            1                 96
D62V8, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            0                 69
  CLUS_2            1                213
  CLUS_3            4                186
D62V9, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            1                114
  CLUS_2            1                190
  CLUS_3            2                167
D62V10, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            0                 35
  CLUS_2            3                157
  CLUS_3            1                279
D62V11, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            1                 49
  CLUS_2            1                 88
  CLUS_3            2                 72
D62V12, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            3                 54
  CLUS_2            0                 92
  CLUS_3            1                 63

Clustering(63) Variable = 17p loss
D63V1, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            0                 33
  CLUS_2            3                 21
  CLUS_3            6                  7
D63V2, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            6                  8
  CLUS_2            0                 32
  CLUS_3            3                 21
D63V3, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           15                149
  CLUS_2            0                216
  CLUS_3           11                113
D63V4, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            5                 94
  CLUS_2            3                116
  CLUS_3            2                 69
D63V5, multiclass
D63V6, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            2                184
  CLUS_2            4                148
  CLUS_3           15                 94
D63V7, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            0                197
  CLUS_2           12                167
  CLUS_3           11                 86
D63V8, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           12                 57
  CLUS_2            0                214
  CLUS_3           11                179
D63V9, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            3                112
  CLUS_2            1                190
  CLUS_3           21                148
D63V10, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           12                 23
  CLUS_2            7                153
  CLUS_3            6                274
D63V11, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            1                 49
  CLUS_2            2                 87
  CLUS_3            7                 67
D63V12, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            7                 50
  CLUS_2            1                 91
  CLUS_3            2                 62

Clustering(64) Variable = 17q loss
D64V1, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            0                 33
  CLUS_2            2                 22
  CLUS_3            5                  8
D64V2, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            5                  9
  CLUS_2            0                 32
  CLUS_3            2                 22
D64V3, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            2                162
  CLUS_2            0                216
  CLUS_3           10                114
D64V4, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            0                 99
  CLUS_2            2                117
  CLUS_3            1                 70
D64V5, multiclass
D64V6, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            0                186
  CLUS_2            0                152
  CLUS_3            8                101
D64V7, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            0                197
  CLUS_2            1                178
  CLUS_3            9                 88
D64V8, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            9                 60
  CLUS_2            0                214
  CLUS_3            1                189
D64V9, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            1                114
  CLUS_2            0                191
  CLUS_3           11                158
D64V10, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1           10                 25
  CLUS_2            0                160
  CLUS_3            2                278
D64V11, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            1                 49
  CLUS_2            1                 88
  CLUS_3            1                 73
D64V12, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            3                 54
  CLUS_2            0                 92
  CLUS_3            0                 64

Clustering(65) Variable = 18p loss
D65V1, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            2                 31
  CLUS_2            5                 19
  CLUS_3            1                 12
D65V2, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            2                 12
  CLUS_2            2                 30
  CLUS_3            4                 20
D65V3, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           28                136
  CLUS_2            8                208
  CLUS_3           10                114
D65V4, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           12                 87
  CLUS_2            4                115
  CLUS_3            8                 63
D65V5, multiclass
D65V6, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            8                178
  CLUS_2           19                133
  CLUS_3           15                 94
D65V7, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            8                189
  CLUS_2           32                147
  CLUS_3            4                 93
D65V8, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            7                 62
  CLUS_2            8                206
  CLUS_3           29                161
D65V9, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           10                105
  CLUS_2            8                183
  CLUS_3           28                141
D65V10, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            9                 26
  CLUS_2           18                142
  CLUS_3           19                261
D65V11, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            4                 46
  CLUS_2            3                 86
  CLUS_3           16                 58
D65V12, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           13                 44
  CLUS_2            2                 90
  CLUS_3            8                 56

Clustering(66) Variable = 18q loss
D66V1, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            2                 31
  CLUS_2            5                 19
  CLUS_3            2                 11
D66V2, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            3                 11
  CLUS_2            2                 30
  CLUS_3            4                 20
D66V3, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           29                135
  CLUS_2            9                207
  CLUS_3           10                114
D66V4, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           13                 86
  CLUS_2            5                114
  CLUS_3            8                 63
D66V5, multiclass
D66V6, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           10                176
  CLUS_2           19                133
  CLUS_3           16                 93
D66V7, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            9                188
  CLUS_2           32                147
  CLUS_3            5                 92
D66V8, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            9                 60
  CLUS_2            9                205
  CLUS_3           28                162
D66V9, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           11                104
  CLUS_2            9                182
  CLUS_3           28                141
D66V10, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            9                 26
  CLUS_2           18                142
  CLUS_3           21                259
D66V11, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            3                 47
  CLUS_2            3                 86
  CLUS_3           16                 58
D66V12, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           13                 44
  CLUS_2            3                 89
  CLUS_3            6                 58

Clustering(67) Variable = 19p loss
D67V1, multiclass
[1] "Remove cluster labels:" "19P LOSS CNV"          
clus
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3374         TCGA-A3-3378 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3380         TCGA-A3-3382         TCGA-A3-3383 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3427         TCGA-AK-3440 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AK-3443         TCGA-AK-3444         TCGA-AK-3447 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AK-3453         TCGA-AK-3455         TCGA-AK-3456 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AK-3465         TCGA-AS-3777         TCGA-AS-3778 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B2-3923         TCGA-B2-3924         TCGA-B2-4098 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B2-4099         TCGA-B2-4102         TCGA-B8-4143 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B8-4148         TCGA-B8-4151         TCGA-B8-4154 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B8-4619         TCGA-B8-4620         TCGA-BP-4161 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4162         TCGA-BP-4163         TCGA-BP-4167 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
D67V2, multiclass
[1] "Remove cluster labels:" "19P LOSS CNV"          
clus
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3374         TCGA-A3-3378 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3380         TCGA-A3-3382         TCGA-A3-3383 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3427         TCGA-AK-3440 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AK-3443         TCGA-AK-3444         TCGA-AK-3447 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AK-3453         TCGA-AK-3455         TCGA-AK-3456 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AK-3465         TCGA-AS-3777         TCGA-AS-3778 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B2-3923         TCGA-B2-3924         TCGA-B2-4098 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B2-4099         TCGA-B2-4102         TCGA-B8-4143 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B8-4148         TCGA-B8-4151         TCGA-B8-4154 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B8-4619         TCGA-B8-4620         TCGA-BP-4161 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4162         TCGA-BP-4163         TCGA-BP-4167 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
D67V3, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            3                161
  CLUS_2            0                216
  CLUS_3            1                123
D67V4, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            2                 97
  CLUS_2            0                119
  CLUS_3            1                 70
D67V5, multiclass
D67V6, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            0                186
  CLUS_2            1                151
  CLUS_3            3                106
D67V7, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                196
  CLUS_2            1                178
  CLUS_3            2                 95
D67V8, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            0                 69
  CLUS_2            1                213
  CLUS_3            3                187
D67V9, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                114
  CLUS_2            1                190
  CLUS_3            2                167
D67V10, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            0                 35
  CLUS_2            3                157
  CLUS_3            1                279
D67V11, multiclass
[1] "Remove cluster labels:" "19P LOSS CNV"          
clus
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 1                212 
        TCGA-A3-3317         TCGA-A3-3358         TCGA-A3-3387 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AK-3440         TCGA-AK-3458         TCGA-AK-3465 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-4698         TCGA-B0-4700         TCGA-B0-4706 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-4710         TCGA-B0-4712         TCGA-B0-4810 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-4811         TCGA-B0-4815         TCGA-B0-4816 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-4818         TCGA-B0-4821         TCGA-B0-4833 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-4834         TCGA-B0-4836         TCGA-B0-4837 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-4852         TCGA-B0-5075         TCGA-B0-5080 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-5084         TCGA-B0-5085         TCGA-B0-5088 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-5399         TCGA-B0-5400         TCGA-B0-5402 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-5690         TCGA-B0-5691         TCGA-B0-5692 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-5693         TCGA-B0-5694         TCGA-B0-5695 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-5696         TCGA-B0-5697         TCGA-B0-5698 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-5699         TCGA-B0-5701         TCGA-B0-5702 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-5703         TCGA-B0-5705         TCGA-B0-5706 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-5709         TCGA-B0-5710         TCGA-B0-5711 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-5712         TCGA-B0-5713         TCGA-B0-5812 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B2-5633         TCGA-B2-5635         TCGA-B2-5639 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B2-5641         TCGA-B4-5377         TCGA-B4-5378 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B4-5832         TCGA-B4-5834         TCGA-B4-5835 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B4-5836         TCGA-B4-5838         TCGA-B4-5843 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B4-5844         TCGA-B8-4146         TCGA-B8-4153 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B8-4621         TCGA-B8-5545         TCGA-B8-5546 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B8-5549         TCGA-B8-5550         TCGA-B8-5551 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B8-5552         TCGA-B8-5553         TCGA-BP-4173 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4331         TCGA-BP-4340         TCGA-BP-4759 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4761         TCGA-BP-4771         TCGA-BP-4787 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4789         TCGA-BP-4790         TCGA-BP-4797 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4804         TCGA-BP-4807         TCGA-BP-4959 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4960         TCGA-BP-4961         TCGA-BP-4965 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4967         TCGA-BP-4968         TCGA-BP-4969 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4970         TCGA-BP-4971         TCGA-BP-4973 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4974         TCGA-BP-4975         TCGA-BP-4976 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4977         TCGA-BP-4981         TCGA-BP-4982 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4985         TCGA-BP-4986         TCGA-BP-4987 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4988         TCGA-BP-4989         TCGA-BP-4992 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4994         TCGA-BP-4995         TCGA-BP-4998 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-5000         TCGA-BP-5001         TCGA-BP-5007 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-5008         TCGA-BP-5009         TCGA-CJ-4635 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-4870         TCGA-CJ-4875         TCGA-CJ-4876 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-4878         TCGA-CJ-4881         TCGA-CJ-4887 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-4888         TCGA-CJ-4889         TCGA-CJ-4890 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-4891         TCGA-CJ-4895         TCGA-CJ-4899 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-4900         TCGA-CJ-5671         TCGA-CJ-5672 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-5675         TCGA-CJ-5676         TCGA-CJ-5677 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-5678         TCGA-CJ-5679         TCGA-CJ-5680 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-5681         TCGA-CJ-5682         TCGA-CJ-5683 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-5684         TCGA-CJ-5686         TCGA-CJ-5689 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-6027         TCGA-CJ-6028         TCGA-CJ-6030 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-6031         TCGA-CJ-6032         TCGA-CJ-6033 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CW-5580         TCGA-CW-5581         TCGA-CW-5583 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CW-5584         TCGA-CW-5585         TCGA-CW-5587 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CW-5588         TCGA-CW-5589         TCGA-CW-5591 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CW-6087         TCGA-CW-6088         TCGA-CW-6090 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CW-6093         TCGA-CW-6097         TCGA-CZ-4854 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-4857         TCGA-CZ-4858         TCGA-CZ-4860 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-4863         TCGA-CZ-4864         TCGA-CZ-4865 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-4866         TCGA-CZ-5451         TCGA-CZ-5452 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-5453         TCGA-CZ-5454         TCGA-CZ-5455 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-5456         TCGA-CZ-5457         TCGA-CZ-5458 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-5459         TCGA-CZ-5460         TCGA-CZ-5461 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-5462         TCGA-CZ-5463         TCGA-CZ-5464 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-5465         TCGA-CZ-5466         TCGA-CZ-5467 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-5468         TCGA-CZ-5469         TCGA-CZ-5470 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-5982         TCGA-CZ-5984         TCGA-CZ-5985 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-5986         TCGA-CZ-5987         TCGA-CZ-5988 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-5989         TCGA-DV-5565         TCGA-DV-5566 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DV-5567         TCGA-DV-5568         TCGA-DV-5569 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DV-5573         TCGA-DV-5574         TCGA-DV-5575 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DV-5576         TCGA-EU-5904         TCGA-EU-5905 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EU-5906         TCGA-EU-5907 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
D67V12, multiclass
[1] "Remove cluster labels:" "19P LOSS CNV"          
clus
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 1                212 
        TCGA-A3-3317         TCGA-A3-3358         TCGA-A3-3387 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AK-3440         TCGA-AK-3458         TCGA-AK-3465 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-4698         TCGA-B0-4700         TCGA-B0-4706 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-4710         TCGA-B0-4712         TCGA-B0-4810 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-4811         TCGA-B0-4815         TCGA-B0-4816 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-4818         TCGA-B0-4821         TCGA-B0-4833 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-4834         TCGA-B0-4836         TCGA-B0-4837 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-4852         TCGA-B0-5075         TCGA-B0-5080 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-5084         TCGA-B0-5085         TCGA-B0-5088 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-5399         TCGA-B0-5400         TCGA-B0-5402 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-5690         TCGA-B0-5691         TCGA-B0-5692 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-5693         TCGA-B0-5694         TCGA-B0-5695 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-5696         TCGA-B0-5697         TCGA-B0-5698 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-5699         TCGA-B0-5701         TCGA-B0-5702 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-5703         TCGA-B0-5705         TCGA-B0-5706 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-5709         TCGA-B0-5710         TCGA-B0-5711 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B0-5712         TCGA-B0-5713         TCGA-B0-5812 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B2-5633         TCGA-B2-5635         TCGA-B2-5639 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B2-5641         TCGA-B4-5377         TCGA-B4-5378 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B4-5832         TCGA-B4-5834         TCGA-B4-5835 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B4-5836         TCGA-B4-5838         TCGA-B4-5843 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B4-5844         TCGA-B8-4146         TCGA-B8-4153 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B8-4621         TCGA-B8-5545         TCGA-B8-5546 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B8-5549         TCGA-B8-5550         TCGA-B8-5551 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B8-5552         TCGA-B8-5553         TCGA-BP-4173 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4331         TCGA-BP-4340         TCGA-BP-4759 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4761         TCGA-BP-4771         TCGA-BP-4787 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4789         TCGA-BP-4790         TCGA-BP-4797 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4804         TCGA-BP-4807         TCGA-BP-4959 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4960         TCGA-BP-4961         TCGA-BP-4965 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4967         TCGA-BP-4968         TCGA-BP-4969 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4970         TCGA-BP-4971         TCGA-BP-4973 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4974         TCGA-BP-4975         TCGA-BP-4976 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4977         TCGA-BP-4981         TCGA-BP-4982 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4985         TCGA-BP-4986         TCGA-BP-4987 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4988         TCGA-BP-4989         TCGA-BP-4992 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4994         TCGA-BP-4995         TCGA-BP-4998 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-5000         TCGA-BP-5001         TCGA-BP-5007 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-5008         TCGA-BP-5009         TCGA-CJ-4635 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-4870         TCGA-CJ-4875         TCGA-CJ-4876 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-4878         TCGA-CJ-4881         TCGA-CJ-4887 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-4888         TCGA-CJ-4889         TCGA-CJ-4890 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-4891         TCGA-CJ-4895         TCGA-CJ-4899 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-4900         TCGA-CJ-5671         TCGA-CJ-5672 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-5675         TCGA-CJ-5676         TCGA-CJ-5677 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-5678         TCGA-CJ-5679         TCGA-CJ-5680 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-5681         TCGA-CJ-5682         TCGA-CJ-5683 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-5684         TCGA-CJ-5686         TCGA-CJ-5689 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-6027         TCGA-CJ-6028         TCGA-CJ-6030 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-6031         TCGA-CJ-6032         TCGA-CJ-6033 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CW-5580         TCGA-CW-5581         TCGA-CW-5583 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CW-5584         TCGA-CW-5585         TCGA-CW-5587 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CW-5588         TCGA-CW-5589         TCGA-CW-5591 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CW-6087         TCGA-CW-6088         TCGA-CW-6090 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CW-6093         TCGA-CW-6097         TCGA-CZ-4854 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-4857         TCGA-CZ-4858         TCGA-CZ-4860 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-4863         TCGA-CZ-4864         TCGA-CZ-4865 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-4866         TCGA-CZ-5451         TCGA-CZ-5452 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-5453         TCGA-CZ-5454         TCGA-CZ-5455 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-5456         TCGA-CZ-5457         TCGA-CZ-5458 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-5459         TCGA-CZ-5460         TCGA-CZ-5461 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-5462         TCGA-CZ-5463         TCGA-CZ-5464 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-5465         TCGA-CZ-5466         TCGA-CZ-5467 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-5468         TCGA-CZ-5469         TCGA-CZ-5470 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-5982         TCGA-CZ-5984         TCGA-CZ-5985 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-5986         TCGA-CZ-5987         TCGA-CZ-5988 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-5989         TCGA-DV-5565         TCGA-DV-5566 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DV-5567         TCGA-DV-5568         TCGA-DV-5569 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DV-5573         TCGA-DV-5574         TCGA-DV-5575 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DV-5576         TCGA-EU-5904         TCGA-EU-5905 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EU-5906         TCGA-EU-5907 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 

Clustering(68) Variable = 20p loss
D68V1, multiclass
[1] "Remove cluster labels:" "20P LOSS CNV"          
clus
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3320         TCGA-A3-3322 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3323         TCGA-A3-3324         TCGA-A3-3325 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3326         TCGA-A3-3331         TCGA-A3-3335 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3336         TCGA-A3-3343         TCGA-A3-3346 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3347         TCGA-A3-3349         TCGA-A3-3351 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3352         TCGA-A3-3359         TCGA-A3-3362 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3363         TCGA-A3-3365         TCGA-A3-3372 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3374         TCGA-A3-3378         TCGA-A3-3380 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3382         TCGA-A3-3383         TCGA-AK-3426 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AK-3427         TCGA-AK-3440         TCGA-AK-3443 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AK-3444         TCGA-AK-3447         TCGA-AK-3453 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AK-3455         TCGA-AK-3456         TCGA-AK-3465 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
D68V2, multiclass
[1] "Remove cluster labels:" "20P LOSS CNV"          
clus
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3320         TCGA-A3-3322 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3323         TCGA-A3-3324         TCGA-A3-3325 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3326         TCGA-A3-3331         TCGA-A3-3335 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3336         TCGA-A3-3343         TCGA-A3-3346 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3347         TCGA-A3-3349         TCGA-A3-3351 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3352         TCGA-A3-3359         TCGA-A3-3362 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3363         TCGA-A3-3365         TCGA-A3-3372 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3374         TCGA-A3-3378         TCGA-A3-3380 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3382         TCGA-A3-3383         TCGA-AK-3426 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AK-3427         TCGA-AK-3440         TCGA-AK-3443 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AK-3444         TCGA-AK-3447         TCGA-AK-3453 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AK-3455         TCGA-AK-3456         TCGA-AK-3465 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
D68V3, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            4                160
  CLUS_2            2                214
  CLUS_3            0                124
D68V4, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            1                 98
  CLUS_2            1                118
  CLUS_3            1                 70
D68V5, multiclass
D68V6, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            2                184
  CLUS_2            2                150
  CLUS_3            2                107
D68V7, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            1                196
  CLUS_2            4                175
  CLUS_3            1                 96
D68V8, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            1                 68
  CLUS_2            2                212
  CLUS_3            3                187
D68V9, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            2                113
  CLUS_2            0                191
  CLUS_3            4                165
D68V10, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            1                 34
  CLUS_2            3                157
  CLUS_3            2                278
D68V11, multiclass
[1] "Remove cluster labels:" "20P LOSS CNV"          
clus
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 2                211 
        TCGA-A3-3317         TCGA-A3-3358         TCGA-A3-3387 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AK-3440         TCGA-AK-3458         TCGA-AK-3465 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-4698         TCGA-B0-4700         TCGA-B0-4706 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-4710         TCGA-B0-4712         TCGA-B0-4810 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-4811         TCGA-B0-4815         TCGA-B0-4816 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-4818         TCGA-B0-4833         TCGA-B0-4834 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-4836         TCGA-B0-4837         TCGA-B0-4852 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-5075         TCGA-B0-5080         TCGA-B0-5084 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-5085         TCGA-B0-5088         TCGA-B0-5399 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-5400         TCGA-B0-5402         TCGA-B0-5690 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-5691         TCGA-B0-5692         TCGA-B0-5693 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-5694         TCGA-B0-5695         TCGA-B0-5696 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-5697         TCGA-B0-5698         TCGA-B0-5699 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-5701         TCGA-B0-5702         TCGA-B0-5703 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-5705         TCGA-B0-5706         TCGA-B0-5709 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-5710         TCGA-B0-5711         TCGA-B0-5712 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-5713         TCGA-B0-5812         TCGA-B2-5633 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B2-5635         TCGA-B2-5639         TCGA-B2-5641 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B4-5377         TCGA-B4-5378         TCGA-B4-5832 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B4-5834         TCGA-B4-5835         TCGA-B4-5836 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B4-5838         TCGA-B4-5843         TCGA-B4-5844 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B8-4146         TCGA-B8-4153         TCGA-B8-4621 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B8-5545         TCGA-B8-5546         TCGA-B8-5549 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B8-5550         TCGA-B8-5551         TCGA-B8-5552 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B8-5553         TCGA-BP-4173         TCGA-BP-4331 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4340         TCGA-BP-4759         TCGA-BP-4761 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4770         TCGA-BP-4771         TCGA-BP-4787 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4789         TCGA-BP-4790         TCGA-BP-4797 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4804         TCGA-BP-4807         TCGA-BP-4959 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4960         TCGA-BP-4961         TCGA-BP-4965 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4967         TCGA-BP-4968         TCGA-BP-4969 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4970         TCGA-BP-4971         TCGA-BP-4973 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4974         TCGA-BP-4975         TCGA-BP-4976 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4977         TCGA-BP-4981         TCGA-BP-4982 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4985         TCGA-BP-4986         TCGA-BP-4987 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4988         TCGA-BP-4989         TCGA-BP-4992 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4994         TCGA-BP-4995         TCGA-BP-4998 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-5001         TCGA-BP-5007         TCGA-BP-5008 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-5009         TCGA-CJ-4635         TCGA-CJ-4870 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-4875         TCGA-CJ-4876         TCGA-CJ-4878 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-4881         TCGA-CJ-4887         TCGA-CJ-4888 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-4889         TCGA-CJ-4890         TCGA-CJ-4891 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-4895         TCGA-CJ-4899         TCGA-CJ-4900 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-5671         TCGA-CJ-5672         TCGA-CJ-5675 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-5676         TCGA-CJ-5677         TCGA-CJ-5678 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-5679         TCGA-CJ-5680         TCGA-CJ-5681 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-5682         TCGA-CJ-5683         TCGA-CJ-5684 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-5686         TCGA-CJ-5689         TCGA-CJ-6027 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-6028         TCGA-CJ-6030         TCGA-CJ-6031 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-6032         TCGA-CJ-6033         TCGA-CW-5580 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CW-5581         TCGA-CW-5583         TCGA-CW-5584 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CW-5585         TCGA-CW-5587         TCGA-CW-5588 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CW-5589         TCGA-CW-5591         TCGA-CW-6087 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CW-6088         TCGA-CW-6090         TCGA-CW-6093 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CW-6097         TCGA-CZ-4854         TCGA-CZ-4857 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-4858         TCGA-CZ-4860         TCGA-CZ-4863 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-4864         TCGA-CZ-4865         TCGA-CZ-4866 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-5451         TCGA-CZ-5452         TCGA-CZ-5453 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-5454         TCGA-CZ-5455         TCGA-CZ-5456 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-5457         TCGA-CZ-5458         TCGA-CZ-5459 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-5460         TCGA-CZ-5461         TCGA-CZ-5462 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-5463         TCGA-CZ-5464         TCGA-CZ-5465 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-5466         TCGA-CZ-5467         TCGA-CZ-5468 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-5469         TCGA-CZ-5470         TCGA-CZ-5982 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-5984         TCGA-CZ-5985         TCGA-CZ-5986 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-5987         TCGA-CZ-5988         TCGA-CZ-5989 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DV-5565         TCGA-DV-5566         TCGA-DV-5567 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DV-5568         TCGA-DV-5569         TCGA-DV-5573 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DV-5574         TCGA-DV-5575         TCGA-DV-5576 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EU-5904         TCGA-EU-5905         TCGA-EU-5906 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EU-5907 
"20P LOSS WILD-TYPE" 
D68V12, multiclass
[1] "Remove cluster labels:" "20P LOSS CNV"          
clus
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 2                211 
        TCGA-A3-3317         TCGA-A3-3358         TCGA-A3-3387 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AK-3440         TCGA-AK-3458         TCGA-AK-3465 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-4698         TCGA-B0-4700         TCGA-B0-4706 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-4710         TCGA-B0-4712         TCGA-B0-4810 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-4811         TCGA-B0-4815         TCGA-B0-4816 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-4818         TCGA-B0-4833         TCGA-B0-4834 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-4836         TCGA-B0-4837         TCGA-B0-4852 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-5075         TCGA-B0-5080         TCGA-B0-5084 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-5085         TCGA-B0-5088         TCGA-B0-5399 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-5400         TCGA-B0-5402         TCGA-B0-5690 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-5691         TCGA-B0-5692         TCGA-B0-5693 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-5694         TCGA-B0-5695         TCGA-B0-5696 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-5697         TCGA-B0-5698         TCGA-B0-5699 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-5701         TCGA-B0-5702         TCGA-B0-5703 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-5705         TCGA-B0-5706         TCGA-B0-5709 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-5710         TCGA-B0-5711         TCGA-B0-5712 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-5713         TCGA-B0-5812         TCGA-B2-5633 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B2-5635         TCGA-B2-5639         TCGA-B2-5641 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B4-5377         TCGA-B4-5378         TCGA-B4-5832 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B4-5834         TCGA-B4-5835         TCGA-B4-5836 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B4-5838         TCGA-B4-5843         TCGA-B4-5844 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B8-4146         TCGA-B8-4153         TCGA-B8-4621 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B8-5545         TCGA-B8-5546         TCGA-B8-5549 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B8-5550         TCGA-B8-5551         TCGA-B8-5552 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B8-5553         TCGA-BP-4173         TCGA-BP-4331 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4340         TCGA-BP-4759         TCGA-BP-4761 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4770         TCGA-BP-4771         TCGA-BP-4787 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4789         TCGA-BP-4790         TCGA-BP-4797 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4804         TCGA-BP-4807         TCGA-BP-4959 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4960         TCGA-BP-4961         TCGA-BP-4965 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4967         TCGA-BP-4968         TCGA-BP-4969 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4970         TCGA-BP-4971         TCGA-BP-4973 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4974         TCGA-BP-4975         TCGA-BP-4976 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4977         TCGA-BP-4981         TCGA-BP-4982 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4985         TCGA-BP-4986         TCGA-BP-4987 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4988         TCGA-BP-4989         TCGA-BP-4992 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4994         TCGA-BP-4995         TCGA-BP-4998 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-5001         TCGA-BP-5007         TCGA-BP-5008 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-5009         TCGA-CJ-4635         TCGA-CJ-4870 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-4875         TCGA-CJ-4876         TCGA-CJ-4878 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-4881         TCGA-CJ-4887         TCGA-CJ-4888 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-4889         TCGA-CJ-4890         TCGA-CJ-4891 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-4895         TCGA-CJ-4899         TCGA-CJ-4900 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-5671         TCGA-CJ-5672         TCGA-CJ-5675 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-5676         TCGA-CJ-5677         TCGA-CJ-5678 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-5679         TCGA-CJ-5680         TCGA-CJ-5681 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-5682         TCGA-CJ-5683         TCGA-CJ-5684 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-5686         TCGA-CJ-5689         TCGA-CJ-6027 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-6028         TCGA-CJ-6030         TCGA-CJ-6031 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-6032         TCGA-CJ-6033         TCGA-CW-5580 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CW-5581         TCGA-CW-5583         TCGA-CW-5584 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CW-5585         TCGA-CW-5587         TCGA-CW-5588 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CW-5589         TCGA-CW-5591         TCGA-CW-6087 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CW-6088         TCGA-CW-6090         TCGA-CW-6093 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CW-6097         TCGA-CZ-4854         TCGA-CZ-4857 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-4858         TCGA-CZ-4860         TCGA-CZ-4863 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-4864         TCGA-CZ-4865         TCGA-CZ-4866 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-5451         TCGA-CZ-5452         TCGA-CZ-5453 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-5454         TCGA-CZ-5455         TCGA-CZ-5456 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-5457         TCGA-CZ-5458         TCGA-CZ-5459 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-5460         TCGA-CZ-5461         TCGA-CZ-5462 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-5463         TCGA-CZ-5464         TCGA-CZ-5465 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-5466         TCGA-CZ-5467         TCGA-CZ-5468 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-5469         TCGA-CZ-5470         TCGA-CZ-5982 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-5984         TCGA-CZ-5985         TCGA-CZ-5986 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-5987         TCGA-CZ-5988         TCGA-CZ-5989 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DV-5565         TCGA-DV-5566         TCGA-DV-5567 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DV-5568         TCGA-DV-5569         TCGA-DV-5573 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DV-5574         TCGA-DV-5575         TCGA-DV-5576 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EU-5904         TCGA-EU-5905         TCGA-EU-5906 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EU-5907 
"20P LOSS WILD-TYPE" 

Clustering(69) Variable = 21q loss
D69V1, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            1                 32
  CLUS_2            1                 23
  CLUS_3            4                  9
D69V2, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            4                 10
  CLUS_2            1                 31
  CLUS_3            1                 23
D69V3, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1           11                153
  CLUS_2            5                211
  CLUS_3           18                106
D69V4, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1           10                 89
  CLUS_2            5                114
  CLUS_3            7                 64
D69V5, multiclass
D69V6, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            7                179
  CLUS_2            7                145
  CLUS_3           12                 97
D69V7, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            8                189
  CLUS_2            7                172
  CLUS_3           14                 83
D69V8, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1           14                 55
  CLUS_2            6                208
  CLUS_3            9                181
D69V9, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            6                109
  CLUS_2           10                181
  CLUS_3           16                153
D69V10, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1           11                 24
  CLUS_2            8                152
  CLUS_3           13                267
D69V11, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            4                 46
  CLUS_2            9                 80
  CLUS_3            4                 70
D69V12, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            8                 49
  CLUS_2            4                 88
  CLUS_3            5                 59

Clustering(70) Variable = 22q loss
D70V1, multiclass
D70V2, multiclass
D70V3, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            8                156
  CLUS_2            0                216
  CLUS_3            4                120
D70V4, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            6                 93
  CLUS_2            0                119
  CLUS_3            2                 69
D70V5, multiclass
D70V6, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            3                183
  CLUS_2            6                146
  CLUS_3            2                107
D70V7, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            1                196
  CLUS_2           10                169
  CLUS_3            0                 97
D70V8, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            0                 69
  CLUS_2            2                212
  CLUS_3            9                181
D70V9, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            1                114
  CLUS_2            4                187
  CLUS_3            6                163
D70V10, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            1                 34
  CLUS_2            5                155
  CLUS_3            5                275
D70V11, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            1                 49
  CLUS_2            2                 87
  CLUS_3            4                 70
D70V12, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            4                 53
  CLUS_2            1                 91
  CLUS_3            2                 62

Clustering(71) Variable = Xq loss
D71V1, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           1                32
  CLUS_2           2                22
  CLUS_3           2                11
D71V2, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           2                12
  CLUS_2           1                31
  CLUS_3           2                22
D71V3, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           4               160
  CLUS_2           3               213
  CLUS_3           3               121
D71V4, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           2                97
  CLUS_2           1               118
  CLUS_3           2                69
D71V5, multiclass
D71V6, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           1               185
  CLUS_2           2               150
  CLUS_3           3               106
D71V7, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           1               196
  CLUS_2           2               177
  CLUS_3           4                93
D71V8, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           3                66
  CLUS_2           0               214
  CLUS_3           4               186
D71V9, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           0               115
  CLUS_2           2               189
  CLUS_3           7               162
D71V10, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           3                32
  CLUS_2           2               158
  CLUS_3           4               276
D71V11, multiclass
[1] "Remove cluster labels:" "XQ LOSS CNV"           
clus
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                2               211 
       TCGA-A3-3317        TCGA-A3-3358        TCGA-A3-3387        TCGA-AK-3458 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AK-3465        TCGA-B0-4698        TCGA-B0-4700        TCGA-B0-4706 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B0-4710        TCGA-B0-4712        TCGA-B0-4810        TCGA-B0-4811 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B0-4815        TCGA-B0-4816        TCGA-B0-4818        TCGA-B0-4821 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B0-4833        TCGA-B0-4834        TCGA-B0-4836        TCGA-B0-4837 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B0-4852        TCGA-B0-5075        TCGA-B0-5080        TCGA-B0-5084 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B0-5085        TCGA-B0-5088        TCGA-B0-5399        TCGA-B0-5400 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B0-5402        TCGA-B0-5690        TCGA-B0-5691        TCGA-B0-5692 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B0-5693        TCGA-B0-5694        TCGA-B0-5695        TCGA-B0-5696 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B0-5697        TCGA-B0-5698        TCGA-B0-5699        TCGA-B0-5701 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B0-5702        TCGA-B0-5703        TCGA-B0-5705        TCGA-B0-5706 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B0-5709        TCGA-B0-5710        TCGA-B0-5711        TCGA-B0-5712 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B0-5713        TCGA-B0-5812        TCGA-B2-5633        TCGA-B2-5635 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B2-5639        TCGA-B2-5641        TCGA-B4-5377        TCGA-B4-5378 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835        TCGA-B4-5836 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844        TCGA-B8-4146 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B8-4153        TCGA-B8-4621        TCGA-B8-5545        TCGA-B8-5546 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B8-5549        TCGA-B8-5550        TCGA-B8-5551        TCGA-B8-5552 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B8-5553        TCGA-BP-4173        TCGA-BP-4331        TCGA-BP-4340 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BP-4759        TCGA-BP-4761        TCGA-BP-4770        TCGA-BP-4771 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BP-4787        TCGA-BP-4789        TCGA-BP-4790        TCGA-BP-4797 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BP-4804        TCGA-BP-4807        TCGA-BP-4959        TCGA-BP-4960 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BP-4961        TCGA-BP-4965        TCGA-BP-4967        TCGA-BP-4968 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BP-4969        TCGA-BP-4970        TCGA-BP-4971        TCGA-BP-4973 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BP-4974        TCGA-BP-4975        TCGA-BP-4976        TCGA-BP-4977 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BP-4981        TCGA-BP-4982        TCGA-BP-4985        TCGA-BP-4986 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BP-4987        TCGA-BP-4988        TCGA-BP-4989        TCGA-BP-4992 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BP-4994        TCGA-BP-4995        TCGA-BP-4998        TCGA-BP-5000 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BP-5001        TCGA-BP-5007        TCGA-BP-5008        TCGA-BP-5009 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CJ-4635        TCGA-CJ-4870        TCGA-CJ-4875        TCGA-CJ-4876 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CJ-4878        TCGA-CJ-4881        TCGA-CJ-4887        TCGA-CJ-4888 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CJ-4889        TCGA-CJ-4890        TCGA-CJ-4891        TCGA-CJ-4895 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CJ-4899        TCGA-CJ-4900        TCGA-CJ-5671        TCGA-CJ-5672 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CJ-5675        TCGA-CJ-5676        TCGA-CJ-5677        TCGA-CJ-5678 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CJ-5679        TCGA-CJ-5680        TCGA-CJ-5681        TCGA-CJ-5682 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CJ-5683        TCGA-CJ-5684        TCGA-CJ-5686        TCGA-CJ-5689 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CJ-6027        TCGA-CJ-6028        TCGA-CJ-6030        TCGA-CJ-6031 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CJ-6032        TCGA-CJ-6033        TCGA-CW-5580        TCGA-CW-5581 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CW-5583        TCGA-CW-5584        TCGA-CW-5585        TCGA-CW-5587 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CW-5588        TCGA-CW-5589        TCGA-CW-5591        TCGA-CW-6087 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CW-6088        TCGA-CW-6090        TCGA-CW-6093        TCGA-CW-6097 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CZ-4854        TCGA-CZ-4857        TCGA-CZ-4858        TCGA-CZ-4860 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CZ-4863        TCGA-CZ-4864        TCGA-CZ-4865        TCGA-CZ-4866 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CZ-5451        TCGA-CZ-5452        TCGA-CZ-5453        TCGA-CZ-5454 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CZ-5455        TCGA-CZ-5456        TCGA-CZ-5457        TCGA-CZ-5459 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CZ-5460        TCGA-CZ-5461        TCGA-CZ-5462        TCGA-CZ-5463 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CZ-5464        TCGA-CZ-5465        TCGA-CZ-5466        TCGA-CZ-5467 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CZ-5468        TCGA-CZ-5469        TCGA-CZ-5470        TCGA-CZ-5982 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CZ-5984        TCGA-CZ-5985        TCGA-CZ-5986        TCGA-CZ-5987 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CZ-5988        TCGA-CZ-5989        TCGA-DV-5565        TCGA-DV-5566 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DV-5567        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5573 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576        TCGA-EU-5904 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D71V12, multiclass
[1] "Remove cluster labels:" "XQ LOSS CNV"           
clus
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                2               211 
       TCGA-A3-3317        TCGA-A3-3358        TCGA-A3-3387        TCGA-AK-3458 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AK-3465        TCGA-B0-4698        TCGA-B0-4700        TCGA-B0-4706 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B0-4710        TCGA-B0-4712        TCGA-B0-4810        TCGA-B0-4811 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B0-4815        TCGA-B0-4816        TCGA-B0-4818        TCGA-B0-4821 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B0-4833        TCGA-B0-4834        TCGA-B0-4836        TCGA-B0-4837 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B0-4852        TCGA-B0-5075        TCGA-B0-5080        TCGA-B0-5084 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B0-5085        TCGA-B0-5088        TCGA-B0-5399        TCGA-B0-5400 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B0-5402        TCGA-B0-5690        TCGA-B0-5691        TCGA-B0-5692 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B0-5693        TCGA-B0-5694        TCGA-B0-5695        TCGA-B0-5696 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B0-5697        TCGA-B0-5698        TCGA-B0-5699        TCGA-B0-5701 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B0-5702        TCGA-B0-5703        TCGA-B0-5705        TCGA-B0-5706 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B0-5709        TCGA-B0-5710        TCGA-B0-5711        TCGA-B0-5712 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B0-5713        TCGA-B0-5812        TCGA-B2-5633        TCGA-B2-5635 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B2-5639        TCGA-B2-5641        TCGA-B4-5377        TCGA-B4-5378 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835        TCGA-B4-5836 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844        TCGA-B8-4146 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B8-4153        TCGA-B8-4621        TCGA-B8-5545        TCGA-B8-5546 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B8-5549        TCGA-B8-5550        TCGA-B8-5551        TCGA-B8-5552 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B8-5553        TCGA-BP-4173        TCGA-BP-4331        TCGA-BP-4340 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BP-4759        TCGA-BP-4761        TCGA-BP-4770        TCGA-BP-4771 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BP-4787        TCGA-BP-4789        TCGA-BP-4790        TCGA-BP-4797 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BP-4804        TCGA-BP-4807        TCGA-BP-4959        TCGA-BP-4960 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BP-4961        TCGA-BP-4965        TCGA-BP-4967        TCGA-BP-4968 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BP-4969        TCGA-BP-4970        TCGA-BP-4971        TCGA-BP-4973 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BP-4974        TCGA-BP-4975        TCGA-BP-4976        TCGA-BP-4977 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BP-4981        TCGA-BP-4982        TCGA-BP-4985        TCGA-BP-4986 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BP-4987        TCGA-BP-4988        TCGA-BP-4989        TCGA-BP-4992 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BP-4994        TCGA-BP-4995        TCGA-BP-4998        TCGA-BP-5000 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BP-5001        TCGA-BP-5007        TCGA-BP-5008        TCGA-BP-5009 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CJ-4635        TCGA-CJ-4870        TCGA-CJ-4875        TCGA-CJ-4876 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CJ-4878        TCGA-CJ-4881        TCGA-CJ-4887        TCGA-CJ-4888 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CJ-4889        TCGA-CJ-4890        TCGA-CJ-4891        TCGA-CJ-4895 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CJ-4899        TCGA-CJ-4900        TCGA-CJ-5671        TCGA-CJ-5672 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CJ-5675        TCGA-CJ-5676        TCGA-CJ-5677        TCGA-CJ-5678 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CJ-5679        TCGA-CJ-5680        TCGA-CJ-5681        TCGA-CJ-5682 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CJ-5683        TCGA-CJ-5684        TCGA-CJ-5686        TCGA-CJ-5689 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CJ-6027        TCGA-CJ-6028        TCGA-CJ-6030        TCGA-CJ-6031 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CJ-6032        TCGA-CJ-6033        TCGA-CW-5580        TCGA-CW-5581 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CW-5583        TCGA-CW-5584        TCGA-CW-5585        TCGA-CW-5587 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CW-5588        TCGA-CW-5589        TCGA-CW-5591        TCGA-CW-6087 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CW-6088        TCGA-CW-6090        TCGA-CW-6093        TCGA-CW-6097 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CZ-4854        TCGA-CZ-4857        TCGA-CZ-4858        TCGA-CZ-4860 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CZ-4863        TCGA-CZ-4864        TCGA-CZ-4865        TCGA-CZ-4866 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CZ-5451        TCGA-CZ-5452        TCGA-CZ-5453        TCGA-CZ-5454 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CZ-5455        TCGA-CZ-5456        TCGA-CZ-5457        TCGA-CZ-5459 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CZ-5460        TCGA-CZ-5461        TCGA-CZ-5462        TCGA-CZ-5463 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CZ-5464        TCGA-CZ-5465        TCGA-CZ-5466        TCGA-CZ-5467 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CZ-5468        TCGA-CZ-5469        TCGA-CZ-5470        TCGA-CZ-5982 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CZ-5984        TCGA-CZ-5985        TCGA-CZ-5986        TCGA-CZ-5987 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CZ-5988        TCGA-CZ-5989        TCGA-DV-5565        TCGA-DV-5566 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DV-5567        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5573 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576        TCGA-EU-5904 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
                           V1                            V2 
                  "MRNA_CNMF"          "MRNA_CHIERARCHICAL" 
                           V3                            V4 
                    "CN_CNMF"            "METHLYATION_CNMF" 
                           V5                            V6 
                  "RPPA_CNMF"          "RPPA_CHIERARCHICAL" 
                           V7                            V8 
               "MRNASEQ_CNMF"       "MRNASEQ_CHIERARCHICAL" 
                           V9                           V10 
                "MIRSEQ_CNMF"        "MIRSEQ_CHIERARCHICAL" 
                          V11                           V12 
         "MIRSEQ_MATURE_CNMF" "MIRSEQ_MATURE_CHIERARCHICAL" 
> q(save="no")
