
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/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_cnvarms_onlysig.2.4053/CNV2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_cnvarms_onlysig.2.4053/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/376725/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/GBM-TP/2909397/1.GDAC_mergedClustering.Finished/GBM-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=GBM-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=GBM-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=584, in cluster file=563, common to both=563
[1] "Reduce the number of clustering variables from 80 to 79."
[1]  79 563
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               40               523 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               40               523 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               45               518 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               45               518 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               20               543 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               20               543 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               18               545 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               18               545 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               30               533 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               30               533 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               30               533 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               30               533 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               15               548 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               15               548 
[1] "4q gain mutation analysis"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               14               549 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               14               549 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               30               533 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               30               533 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               23               540 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               23               540 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7               556 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7               556 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                9               554 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                9               554 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              434               129 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              434               129 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              439               124 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              439               124 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               26               537 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               26               537 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               31               532 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               31               532 
[1] "9p gain mutation analysis"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               17               546 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               17               546 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               34               529 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               34               529 
[1] "10p gain mutation analysis"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                551 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                551 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                559 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                559 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                556 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                556 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                43                520 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                43                520 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                33                530 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                33                530 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 3                560 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 3                560 
[1] "14q gain mutation analysis"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 7                556 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 7                556 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 6                557 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 6                557 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                18                545 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                18                545 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                18                545 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                18                545 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                11                552 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                11                552 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                19                544 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                19                544 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                28                535 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                28                535 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                30                533 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                30                533 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               176                387 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               176                387 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               151                412 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               151                412 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               180                383 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               180                383 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               178                385 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               178                385 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                36                527 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                36                527 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                11                552 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                11                552 
[1] "Xq gain mutation analysis"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4               559 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4               559 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                5               558 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                5               558 
[1] "1q loss mutation analysis"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4               559 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4               559 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               553 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               553 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                9               554 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                9               554 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               22               541 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               22               541 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               16               547 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               16               547 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               26               537 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               26               537 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               25               538 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               25               538 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               21               542 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               21               542 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               20               543 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               20               543 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               47               516 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               47               516 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               80               483 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               80               483 
[1] "7p loss mutation analysis"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                5               558 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                5               558 
[1] "7q loss mutation analysis"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               559 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               559 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               34               529 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               34               529 
[1] "8q loss mutation analysis"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               21               542 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               21               542 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              164               399 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              164               399 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               63               500 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               63               500 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               437                126 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               437                126 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               450                113 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               450                113 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                64                499 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                64                499 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                55                508 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                55                508 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                38                525 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                38                525 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                35                528 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                35                528 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               138                425 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               138                425 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               121                442 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               121                442 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                62                501 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                62                501 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                23                540 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                23                540 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                41                522 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                41                522 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                36                527 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                36                527 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                19                544 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                19                544 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                44                519 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                44                519 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                39                524 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                39                524 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                13                550 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                13                550 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                18                545 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                18                545 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                11                552 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                11                552 
[1] "20q loss mutation analysis"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                10                553 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                10                553 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                25                538 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                25                538 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               140                423 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               140                423 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               11               552 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               11               552 
[1] "data2feature, selection=ALL"
 [1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "MIR_CNMF"             
 [4] "MIR_CHIERARCHICAL"     "CN_CNMF"               "METHLYATION_CNMF"     
 [7] "RPPA_CNMF"             "RPPA_CHIERARCHICAL"    "MRNASEQ_CNMF"         
[10] "MRNASEQ_CHIERARCHICAL"

Input Data has 10 rows and 563 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:'MIR_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MIR_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'METHLYATION_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RPPA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "MIR_CNMF"             
 [4] "MIR_CHIERARCHICAL"     "CN_CNMF"               "METHLYATION_CNMF"     
 [7] "RPPA_CNMF"             "RPPA_CHIERARCHICAL"    "MRNASEQ_CNMF"         
[10] "MRNASEQ_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 563 columns, 0 survival variables, and 10 non-survival variables.
MRNA_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIR_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIR_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain mutation analysis
D1V1, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              14               158
  CLUS_2              10               160
  CLUS_3              10               157
D1V2, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              20               197
  CLUS_2               4               122
  CLUS_3              10               156
D1V3, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              10               129
  CLUS_2              13               144
  CLUS_3               4                68
  CLUS_4               8                96
D1V4, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               9               154
  CLUS_2              20               159
  CLUS_3               6               124
D1V5, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              25               136
  CLUS_2               6               208
  CLUS_3               9               179
D1V6, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               4                34
  CLUS_2               1                19
  CLUS_3               0                24
  CLUS_4               1                26
D1V7, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               3                51
  CLUS_2               2                56
  CLUS_3               3                41
  CLUS_4               5                40
D1V8, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               5                59
  CLUS_2               2                31
  CLUS_3               6                98
D1V9, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2                42
  CLUS_2               8                59
  CLUS_3               3                33
D1V10, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               7                59
  CLUS_2               4                17
  CLUS_3               2                58

Clustering(2) Variable = 1q gain mutation analysis
D2V1, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              15               157
  CLUS_2              14               156
  CLUS_3              10               157
D2V2, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              22               195
  CLUS_2               5               121
  CLUS_3              12               154
D2V3, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               9               130
  CLUS_2              14               143
  CLUS_3               4                68
  CLUS_4              12                92
D2V4, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              12               151
  CLUS_2              19               160
  CLUS_3               8               122
D2V5, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              30               131
  CLUS_2               4               210
  CLUS_3              11               177
D2V6, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               5                33
  CLUS_2               1                19
  CLUS_3               0                24
  CLUS_4               2                25
D2V7, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               4                50
  CLUS_2               3                55
  CLUS_3               4                40
  CLUS_4               5                40
D2V8, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               6                58
  CLUS_2               2                31
  CLUS_3               8                96
D2V9, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               4                40
  CLUS_2               7                60
  CLUS_3               3                33
D2V10, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               7                59
  CLUS_2               4                17
  CLUS_3               3                57

Clustering(3) Variable = 2p gain mutation analysis
D3V1, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               8               164
  CLUS_2               8               162
  CLUS_3               2               165
D3V2, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               9               208
  CLUS_2               3               123
  CLUS_3               6               160
D3V3, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               6               133
  CLUS_2               2               155
  CLUS_3               0                72
  CLUS_4              10                94
D3V4, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              10               153
  CLUS_2               6               173
  CLUS_3               2               128
D3V5, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               9               152
  CLUS_2               5               209
  CLUS_3               6               182
D3V6, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               1                37
  CLUS_2               0                20
  CLUS_3               0                24
  CLUS_4               2                25
D3V7, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               1                53
  CLUS_2               2                56
  CLUS_3               2                42
  CLUS_4               3                42
D3V8, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               2                62
  CLUS_2               0                33
  CLUS_3               6                98
D3V9, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               2                42
  CLUS_2               2                65
  CLUS_3               0                36
D3V10, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               3                63
  CLUS_2               0                21
  CLUS_3               1                59

Clustering(4) Variable = 2q gain mutation analysis
D4V1, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               8               164
  CLUS_2               5               165
  CLUS_3               2               165
D4V2, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               9               208
  CLUS_2               3               123
  CLUS_3               3               163
D4V3, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               6               133
  CLUS_2               0               157
  CLUS_3               0                72
  CLUS_4              10                94
D4V4, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              10               153
  CLUS_2               4               175
  CLUS_3               2               128
D4V5, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               8               153
  CLUS_2               5               209
  CLUS_3               5               183
D4V6, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               1                37
  CLUS_2               0                20
  CLUS_3               0                24
  CLUS_4               2                25
D4V7, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               1                53
  CLUS_2               1                57
  CLUS_3               2                42
  CLUS_4               3                42
D4V8, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               2                62
  CLUS_2               0                33
  CLUS_3               5                99
D4V9, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               1                43
  CLUS_2               2                65
  CLUS_3               0                36
D4V10, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               3                63
  CLUS_2               0                21
  CLUS_3               0                60

Clustering(5) Variable = 3p gain mutation analysis
D5V1, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              11               161
  CLUS_2              15               155
  CLUS_3               2               165
D5V2, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              14               203
  CLUS_2               2               124
  CLUS_3              12               154
D5V3, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               9               130
  CLUS_2               6               151
  CLUS_3               4                68
  CLUS_4               8                96
D5V4, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              11               152
  CLUS_2               8               171
  CLUS_3               8               122
D5V5, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              14               147
  CLUS_2               5               209
  CLUS_3              11               177
D5V6, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                37
  CLUS_2               0                20
  CLUS_3               0                24
  CLUS_4               3                24
D5V7, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2                52
  CLUS_2               2                56
  CLUS_3               0                44
  CLUS_4               3                42
D5V8, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               0                64
  CLUS_2               1                32
  CLUS_3               6                98
D5V9, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3                41
  CLUS_2               4                63
  CLUS_3               1                35
D5V10, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               4                62
  CLUS_2               0                21
  CLUS_3               4                56

Clustering(6) Variable = 3q gain mutation analysis
D6V1, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              11               161
  CLUS_2              15               155
  CLUS_3               2               165
D6V2, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              14               203
  CLUS_2               2               124
  CLUS_3              12               154
D6V3, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               9               130
  CLUS_2               6               151
  CLUS_3               4                68
  CLUS_4               8                96
D6V4, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              10               153
  CLUS_2               9               170
  CLUS_3               8               122
D6V5, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              14               147
  CLUS_2               6               208
  CLUS_3              10               178
D6V6, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               1                37
  CLUS_2               0                20
  CLUS_3               0                24
  CLUS_4               3                24
D6V7, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               2                52
  CLUS_2               2                56
  CLUS_3               0                44
  CLUS_4               3                42
D6V8, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               0                64
  CLUS_2               1                32
  CLUS_3               6                98
D6V9, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                41
  CLUS_2               5                62
  CLUS_3               1                35
D6V10, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               5                61
  CLUS_2               0                21
  CLUS_3               4                56

Clustering(7) Variable = 4p gain mutation analysis
D7V1, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               4               168
  CLUS_2               4               166
  CLUS_3               6               161
D7V2, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               5               212
  CLUS_2               5               121
  CLUS_3               4               162
D7V3, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               6               133
  CLUS_2               6               151
  CLUS_3               1                71
  CLUS_4               1               103
D7V4, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               1               162
  CLUS_2               9               170
  CLUS_3               4               126
D7V5, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               3               158
  CLUS_2               4               210
  CLUS_3               8               180
D7V6, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1               108 
       TCGA-06-0650        TCGA-06-1804        TCGA-06-1806        TCGA-06-5408 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-06-6388 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-6389        TCGA-06-6390        TCGA-06-6391        TCGA-06-6693 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-6694        TCGA-06-6695        TCGA-06-6698        TCGA-06-6699 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-6700        TCGA-06-6701        TCGA-12-5295        TCGA-12-5299 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-12-5301        TCGA-14-0740        TCGA-14-0781        TCGA-14-0862 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-14-1043        TCGA-14-1395        TCGA-14-1450        TCGA-15-1444 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-19-4065        TCGA-19-5947        TCGA-19-5950        TCGA-19-5951 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-19-5952        TCGA-19-5953        TCGA-19-5954        TCGA-19-5955 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-19-5956        TCGA-19-5958        TCGA-19-5959        TCGA-19-5960 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-26-6173 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-26-6174        TCGA-28-2501        TCGA-28-2510        TCGA-28-5204 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-28-5207        TCGA-28-5208        TCGA-28-5209        TCGA-28-5211 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-28-5213        TCGA-28-5214        TCGA-28-5215        TCGA-28-5216 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5219        TCGA-28-5220        TCGA-28-6450 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-32-1979        TCGA-32-1980        TCGA-32-5222        TCGA-41-5651 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4925 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-76-4926        TCGA-76-4928        TCGA-76-4929        TCGA-76-4931 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-76-4934        TCGA-76-4935        TCGA-76-6191        TCGA-76-6192 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-76-6193        TCGA-76-6280        TCGA-76-6282        TCGA-76-6283 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-76-6285        TCGA-76-6286        TCGA-76-6656        TCGA-76-6657 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-76-6660        TCGA-76-6661        TCGA-76-6662        TCGA-76-6663 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-76-6664        TCGA-81-5910        TCGA-81-5911        TCGA-87-5896 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V7, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               3                51
  CLUS_2               1                57
  CLUS_3               0                44
  CLUS_4               1                44
D7V8, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0                64
  CLUS_2               2                31
  CLUS_3               3               101
D7V9, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1               146 
       TCGA-02-0047        TCGA-02-0055        TCGA-02-2483        TCGA-02-2485 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-02-2486        TCGA-06-0125        TCGA-06-0129        TCGA-06-0130 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0132        TCGA-06-0138        TCGA-06-0141        TCGA-06-0157 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0158        TCGA-06-0168        TCGA-06-0178        TCGA-06-0184 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0187        TCGA-06-0190        TCGA-06-0210        TCGA-06-0211 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0219        TCGA-06-0238        TCGA-06-0644        TCGA-06-0645 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0646        TCGA-06-0649        TCGA-06-0686        TCGA-06-0743 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0744        TCGA-06-0745        TCGA-06-0747        TCGA-06-0749 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0750        TCGA-06-0878        TCGA-06-0882        TCGA-06-1804 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-2557        TCGA-06-2558        TCGA-06-2559        TCGA-06-2561 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-2562        TCGA-06-2563        TCGA-06-2564        TCGA-06-2565 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-2567        TCGA-06-2569        TCGA-06-2570        TCGA-06-5408 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-08-0386 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-12-0616        TCGA-12-0618        TCGA-12-0619        TCGA-12-0821 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-12-3650        TCGA-12-3652        TCGA-12-3653        TCGA-12-5295 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-12-5299        TCGA-14-0781        TCGA-14-0787        TCGA-14-0789 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-14-0790        TCGA-14-0817        TCGA-14-1034        TCGA-14-1823 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-14-1825        TCGA-14-1829        TCGA-14-2554        TCGA-15-0742 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-15-1444        TCGA-16-0846        TCGA-16-1045        TCGA-19-1390 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-19-1787        TCGA-19-2619        TCGA-19-2620        TCGA-19-2624 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-19-2625        TCGA-19-2629        TCGA-19-4065        TCGA-19-5960 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-27-1830 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-27-1831        TCGA-27-1832        TCGA-27-1834        TCGA-27-1835 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-27-1837        TCGA-27-2519        TCGA-27-2521        TCGA-27-2523 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-27-2524        TCGA-27-2526        TCGA-27-2528        TCGA-28-1747 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-28-1753        TCGA-28-2509        TCGA-28-2510        TCGA-28-2513 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-28-2514        TCGA-28-5204        TCGA-28-5207        TCGA-28-5208 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-28-5209        TCGA-28-5213        TCGA-28-5215        TCGA-28-5216 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5220        TCGA-32-1970        TCGA-32-1980 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-32-1982        TCGA-32-2615        TCGA-32-2616        TCGA-32-2632 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-32-2634        TCGA-32-2638        TCGA-32-4213        TCGA-32-5222 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-41-2571        TCGA-41-2572        TCGA-41-3915        TCGA-41-4097 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-41-5651        TCGA-76-4925        TCGA-76-4926        TCGA-76-4928 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-76-4929        TCGA-76-4931 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V10, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1               146 
       TCGA-02-0047        TCGA-02-0055        TCGA-02-2483        TCGA-02-2485 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-02-2486        TCGA-06-0125        TCGA-06-0129        TCGA-06-0130 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0132        TCGA-06-0138        TCGA-06-0141        TCGA-06-0157 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0158        TCGA-06-0168        TCGA-06-0178        TCGA-06-0184 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0187        TCGA-06-0190        TCGA-06-0210        TCGA-06-0211 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0219        TCGA-06-0238        TCGA-06-0644        TCGA-06-0645 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0646        TCGA-06-0649        TCGA-06-0686        TCGA-06-0743 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0744        TCGA-06-0745        TCGA-06-0747        TCGA-06-0749 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-0750        TCGA-06-0878        TCGA-06-0882        TCGA-06-1804 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-2557        TCGA-06-2558        TCGA-06-2559        TCGA-06-2561 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-2562        TCGA-06-2563        TCGA-06-2564        TCGA-06-2565 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-2567        TCGA-06-2569        TCGA-06-2570        TCGA-06-5408 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-08-0386 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-12-0616        TCGA-12-0618        TCGA-12-0619        TCGA-12-0821 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-12-3650        TCGA-12-3652        TCGA-12-3653        TCGA-12-5295 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-12-5299        TCGA-14-0781        TCGA-14-0787        TCGA-14-0789 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-14-0790        TCGA-14-0817        TCGA-14-1034        TCGA-14-1823 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-14-1825        TCGA-14-1829        TCGA-14-2554        TCGA-15-0742 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-15-1444        TCGA-16-0846        TCGA-16-1045        TCGA-19-1390 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-19-1787        TCGA-19-2619        TCGA-19-2620        TCGA-19-2624 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-19-2625        TCGA-19-2629        TCGA-19-4065        TCGA-19-5960 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-27-1830 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-27-1831        TCGA-27-1832        TCGA-27-1834        TCGA-27-1835 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-27-1837        TCGA-27-2519        TCGA-27-2521        TCGA-27-2523 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-27-2524        TCGA-27-2526        TCGA-27-2528        TCGA-28-1747 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-28-1753        TCGA-28-2509        TCGA-28-2510        TCGA-28-2513 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-28-2514        TCGA-28-5204        TCGA-28-5207        TCGA-28-5208 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-28-5209        TCGA-28-5213        TCGA-28-5215        TCGA-28-5216 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5220        TCGA-32-1970        TCGA-32-1980 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-32-1982        TCGA-32-2615        TCGA-32-2616        TCGA-32-2632 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-32-2634        TCGA-32-2638        TCGA-32-4213        TCGA-32-5222 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-41-2571        TCGA-41-2572        TCGA-41-3915        TCGA-41-4097 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-41-5651        TCGA-76-4925        TCGA-76-4926        TCGA-76-4928 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-76-4929        TCGA-76-4931 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 

Clustering(8) Variable = 4q gain mutation analysis
D8V1, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               3               169
  CLUS_2               5               165
  CLUS_3               5               162
D8V2, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               4               213
  CLUS_2               4               122
  CLUS_3               5               161
D8V3, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               6               133
  CLUS_2               5               152
  CLUS_3               0                72
  CLUS_4               1               103
D8V4, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               1               162
  CLUS_2               8               171
  CLUS_3               3               127
D8V5, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2               159
  CLUS_2               4               210
  CLUS_3               8               180
D8V6, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               107 
       TCGA-06-0650        TCGA-06-1804        TCGA-06-1806        TCGA-06-5408 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-06-6388 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-6389        TCGA-06-6390        TCGA-06-6391        TCGA-06-6693 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-6694        TCGA-06-6695        TCGA-06-6698        TCGA-06-6699 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-6700        TCGA-06-6701        TCGA-12-5295        TCGA-12-5299 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-12-5301        TCGA-14-0740        TCGA-14-0781        TCGA-14-0862 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-14-1043        TCGA-14-1395        TCGA-14-1450        TCGA-15-1444 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-19-4065        TCGA-19-5947        TCGA-19-5950        TCGA-19-5951 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-19-5952        TCGA-19-5953        TCGA-19-5954        TCGA-19-5955 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-19-5958        TCGA-19-5959        TCGA-19-5960        TCGA-26-1442 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-26-5132        TCGA-26-5133        TCGA-26-5134        TCGA-26-5135 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-26-5136        TCGA-26-5139        TCGA-26-6173        TCGA-26-6174 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-28-2501        TCGA-28-2510        TCGA-28-5204        TCGA-28-5207 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-28-5208        TCGA-28-5209        TCGA-28-5211        TCGA-28-5213 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-28-5214        TCGA-28-5215        TCGA-28-5216        TCGA-28-5218 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-28-5219        TCGA-28-5220        TCGA-28-6450        TCGA-32-1979 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-32-1980        TCGA-32-5222        TCGA-41-5651        TCGA-41-6646 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-74-6573        TCGA-74-6575        TCGA-74-6577        TCGA-74-6578 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-74-6581        TCGA-74-6584        TCGA-76-4925        TCGA-76-4926 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-4934 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-76-4935        TCGA-76-6191        TCGA-76-6192        TCGA-76-6193 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-76-6280        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-76-6286        TCGA-76-6656        TCGA-76-6657        TCGA-76-6660 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-76-6661        TCGA-76-6662        TCGA-76-6663        TCGA-76-6664 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-81-5910        TCGA-81-5911        TCGA-87-5896 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V7, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               3                51
  CLUS_2               1                57
  CLUS_3               0                44
  CLUS_4               1                44
D8V8, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0                64
  CLUS_2               2                31
  CLUS_3               3               101
D8V9, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1               146 
       TCGA-02-0047        TCGA-02-0055        TCGA-02-2483        TCGA-02-2485 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-02-2486        TCGA-06-0125        TCGA-06-0129        TCGA-06-0130 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0132        TCGA-06-0138        TCGA-06-0141        TCGA-06-0157 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0158        TCGA-06-0168        TCGA-06-0178        TCGA-06-0184 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0187        TCGA-06-0190        TCGA-06-0210        TCGA-06-0211 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0219        TCGA-06-0238        TCGA-06-0644        TCGA-06-0645 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0646        TCGA-06-0649        TCGA-06-0686        TCGA-06-0743 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0744        TCGA-06-0745        TCGA-06-0747        TCGA-06-0749 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0750        TCGA-06-0878        TCGA-06-0882        TCGA-06-1804 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-2557        TCGA-06-2558        TCGA-06-2559        TCGA-06-2561 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-2562        TCGA-06-2563        TCGA-06-2564        TCGA-06-2565 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-2567        TCGA-06-2569        TCGA-06-2570        TCGA-06-5408 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-08-0386 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-12-0616        TCGA-12-0618        TCGA-12-0619        TCGA-12-0821 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-12-3650        TCGA-12-3652        TCGA-12-3653        TCGA-12-5295 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-12-5299        TCGA-14-0781        TCGA-14-0787        TCGA-14-0789 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-14-0790        TCGA-14-0817        TCGA-14-1034        TCGA-14-1823 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-14-1825        TCGA-14-1829        TCGA-14-2554        TCGA-15-0742 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-15-1444        TCGA-16-0846        TCGA-16-1045        TCGA-19-1390 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-19-1787        TCGA-19-2619        TCGA-19-2620        TCGA-19-2624 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-19-2625        TCGA-19-2629        TCGA-19-4065        TCGA-19-5960 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-27-1830 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-27-1831        TCGA-27-1832        TCGA-27-1834        TCGA-27-1835 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-27-1837        TCGA-27-2519        TCGA-27-2521        TCGA-27-2523 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-27-2524        TCGA-27-2526        TCGA-27-2528        TCGA-28-1747 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-28-1753        TCGA-28-2509        TCGA-28-2510        TCGA-28-2513 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-28-2514        TCGA-28-5204        TCGA-28-5207        TCGA-28-5208 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-28-5209        TCGA-28-5213        TCGA-28-5215        TCGA-28-5216 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5220        TCGA-32-1970        TCGA-32-1980 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-32-1982        TCGA-32-2615        TCGA-32-2616        TCGA-32-2632 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-32-2634        TCGA-32-2638        TCGA-32-4213        TCGA-32-5222 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-41-2571        TCGA-41-2572        TCGA-41-3915        TCGA-41-4097 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-41-5651        TCGA-76-4925        TCGA-76-4926        TCGA-76-4928 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-76-4929        TCGA-76-4931 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V10, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1               146 
       TCGA-02-0047        TCGA-02-0055        TCGA-02-2483        TCGA-02-2485 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-02-2486        TCGA-06-0125        TCGA-06-0129        TCGA-06-0130 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0132        TCGA-06-0138        TCGA-06-0141        TCGA-06-0157 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0158        TCGA-06-0168        TCGA-06-0178        TCGA-06-0184 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0187        TCGA-06-0190        TCGA-06-0210        TCGA-06-0211 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0219        TCGA-06-0238        TCGA-06-0644        TCGA-06-0645 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0646        TCGA-06-0649        TCGA-06-0686        TCGA-06-0743 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0744        TCGA-06-0745        TCGA-06-0747        TCGA-06-0749 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-0750        TCGA-06-0878        TCGA-06-0882        TCGA-06-1804 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-2557        TCGA-06-2558        TCGA-06-2559        TCGA-06-2561 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-2562        TCGA-06-2563        TCGA-06-2564        TCGA-06-2565 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-2567        TCGA-06-2569        TCGA-06-2570        TCGA-06-5408 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-08-0386 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-12-0616        TCGA-12-0618        TCGA-12-0619        TCGA-12-0821 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-12-3650        TCGA-12-3652        TCGA-12-3653        TCGA-12-5295 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-12-5299        TCGA-14-0781        TCGA-14-0787        TCGA-14-0789 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-14-0790        TCGA-14-0817        TCGA-14-1034        TCGA-14-1823 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-14-1825        TCGA-14-1829        TCGA-14-2554        TCGA-15-0742 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-15-1444        TCGA-16-0846        TCGA-16-1045        TCGA-19-1390 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-19-1787        TCGA-19-2619        TCGA-19-2620        TCGA-19-2624 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-19-2625        TCGA-19-2629        TCGA-19-4065        TCGA-19-5960 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-27-1830 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-27-1831        TCGA-27-1832        TCGA-27-1834        TCGA-27-1835 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-27-1837        TCGA-27-2519        TCGA-27-2521        TCGA-27-2523 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-27-2524        TCGA-27-2526        TCGA-27-2528        TCGA-28-1747 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-28-1753        TCGA-28-2509        TCGA-28-2510        TCGA-28-2513 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-28-2514        TCGA-28-5204        TCGA-28-5207        TCGA-28-5208 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-28-5209        TCGA-28-5213        TCGA-28-5215        TCGA-28-5216 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5220        TCGA-32-1970        TCGA-32-1980 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-32-1982        TCGA-32-2615        TCGA-32-2616        TCGA-32-2632 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-32-2634        TCGA-32-2638        TCGA-32-4213        TCGA-32-5222 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-41-2571        TCGA-41-2572        TCGA-41-3915        TCGA-41-4097 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-41-5651        TCGA-76-4925        TCGA-76-4926        TCGA-76-4928 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-76-4929        TCGA-76-4931 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 

Clustering(9) Variable = 5p gain mutation analysis
D9V1, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              14               158
  CLUS_2               6               164
  CLUS_3               6               161
D9V2, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              14               203
  CLUS_2               7               119
  CLUS_3               5               161
D9V3, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              10               129
  CLUS_2               5               152
  CLUS_3               4                68
  CLUS_4               9                95
D9V4, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              13               150
  CLUS_2              10               169
  CLUS_3               5               125
D9V5, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              17               144
  CLUS_2               6               208
  CLUS_3               7               181
D9V6, multiclass
[1] "Remove cluster labels:" "5P GAIN MUTATED"       
clus
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2               107 
       TCGA-06-0650        TCGA-06-1804        TCGA-06-5408        TCGA-06-5410 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-06-5411        TCGA-06-5412        TCGA-06-5413        TCGA-06-5414 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-06-5415        TCGA-06-5416        TCGA-06-5418        TCGA-06-5856 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-06-5858        TCGA-06-5859        TCGA-06-6388        TCGA-06-6389 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-06-6390        TCGA-06-6391        TCGA-06-6693        TCGA-06-6694 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-06-6695        TCGA-06-6697        TCGA-06-6698        TCGA-06-6699 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-06-6700        TCGA-06-6701        TCGA-12-5295        TCGA-12-5299 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-12-5301        TCGA-14-0740        TCGA-14-0781        TCGA-14-0862 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-14-1043        TCGA-14-1395        TCGA-14-1450        TCGA-15-1444 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-19-4065        TCGA-19-5947        TCGA-19-5950        TCGA-19-5951 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-19-5952        TCGA-19-5953        TCGA-19-5954        TCGA-19-5955 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-19-5956        TCGA-19-5958        TCGA-19-5959        TCGA-19-5960 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-26-6173 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-26-6174        TCGA-28-2501        TCGA-28-2510        TCGA-28-5204 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-28-5207        TCGA-28-5208        TCGA-28-5209        TCGA-28-5211 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-28-5213        TCGA-28-5214        TCGA-28-5215        TCGA-28-5218 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-28-5219        TCGA-28-5220        TCGA-28-6450        TCGA-32-1979 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-32-1980        TCGA-32-5222        TCGA-41-5651        TCGA-41-6646 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-74-6573        TCGA-74-6575        TCGA-74-6577        TCGA-74-6578 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-74-6581        TCGA-74-6584        TCGA-76-4925        TCGA-76-4926 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-4934 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-76-4935        TCGA-76-6191        TCGA-76-6192        TCGA-76-6193 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-76-6280        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-76-6286        TCGA-76-6656        TCGA-76-6657        TCGA-76-6660 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-76-6661        TCGA-76-6662        TCGA-76-6663        TCGA-76-6664 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-81-5910        TCGA-81-5911        TCGA-87-5896 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
D9V7, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               0                54
  CLUS_2               3                55
  CLUS_3               1                43
  CLUS_4               0                45
D9V8, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                62
  CLUS_2               0                33
  CLUS_3               2               102
D9V9, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               1                43
  CLUS_2               5                62
  CLUS_3               0                36
D9V10, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               5                61
  CLUS_2               0                21
  CLUS_3               1                59

Clustering(10) Variable = 5q gain mutation analysis
D10V1, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              12               160
  CLUS_2               3               167
  CLUS_3               5               162
D10V2, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              10               207
  CLUS_2               7               119
  CLUS_3               3               163
D10V3, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               8               131
  CLUS_2               2               155
  CLUS_3               3                69
  CLUS_4               8                96
D10V4, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              11               152
  CLUS_2               8               171
  CLUS_3               2               128
D10V5, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              13               148
  CLUS_2               6               208
  CLUS_3               4               184
D10V6, multiclass
[1] "Remove cluster labels:" "5Q GAIN MUTATED"       
clus
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2               107 
       TCGA-06-0650        TCGA-06-1804        TCGA-06-5408        TCGA-06-5410 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-5411        TCGA-06-5412        TCGA-06-5413        TCGA-06-5414 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-5415        TCGA-06-5416        TCGA-06-5418        TCGA-06-5856 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-5858        TCGA-06-5859        TCGA-06-6388        TCGA-06-6389 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-6390        TCGA-06-6391        TCGA-06-6693        TCGA-06-6694 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-6695        TCGA-06-6697        TCGA-06-6698        TCGA-06-6699 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-6700        TCGA-06-6701        TCGA-12-5295        TCGA-12-5299 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-12-5301        TCGA-14-0740        TCGA-14-0781        TCGA-14-0862 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-14-1043        TCGA-14-1395        TCGA-14-1450        TCGA-15-1444 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-4065        TCGA-19-5947        TCGA-19-5950        TCGA-19-5951 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-5952        TCGA-19-5953        TCGA-19-5954        TCGA-19-5955 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-5956        TCGA-19-5958        TCGA-19-5959        TCGA-19-5960 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-26-6173 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-26-6174        TCGA-28-2501        TCGA-28-2510        TCGA-28-5204 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-28-5207        TCGA-28-5208        TCGA-28-5209        TCGA-28-5211 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-28-5213        TCGA-28-5214        TCGA-28-5215        TCGA-28-5218 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-28-5219        TCGA-28-5220        TCGA-28-6450        TCGA-32-1979 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-32-1980        TCGA-32-5222        TCGA-41-5651        TCGA-41-6646 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-74-6573        TCGA-74-6575        TCGA-74-6577        TCGA-74-6578 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-74-6581        TCGA-74-6584        TCGA-76-4925        TCGA-76-4926 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-4934 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-4935        TCGA-76-6191        TCGA-76-6192        TCGA-76-6193 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-6280        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-6286        TCGA-76-6656        TCGA-76-6657        TCGA-76-6660 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-6661        TCGA-76-6662        TCGA-76-6663        TCGA-76-6664 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-81-5910        TCGA-81-5911        TCGA-87-5896 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
D10V7, multiclass
[1] "Remove cluster labels:" "5Q GAIN MUTATED"       
clus
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2               199 
       TCGA-02-0003        TCGA-02-0011        TCGA-02-0014        TCGA-02-0068 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-02-0069        TCGA-02-0116        TCGA-02-2470        TCGA-02-2485 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-0125        TCGA-06-0126        TCGA-06-0128        TCGA-06-0129 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-0130        TCGA-06-0154        TCGA-06-0155        TCGA-06-0171 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-0189        TCGA-06-0238        TCGA-06-0644        TCGA-06-0650 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-0875        TCGA-06-0876        TCGA-06-0877        TCGA-06-0878 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-0879        TCGA-06-0882        TCGA-06-0939        TCGA-06-1084 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-1086        TCGA-06-1087        TCGA-06-1800        TCGA-06-1802 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-1804        TCGA-06-1805        TCGA-06-2557        TCGA-06-2558 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-2559        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2566        TCGA-06-2567        TCGA-06-2570 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-5408        TCGA-06-5410        TCGA-06-5411        TCGA-06-5412 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-5413        TCGA-06-5414        TCGA-06-5415        TCGA-06-5416 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-5418        TCGA-06-5856        TCGA-06-5858        TCGA-06-5859 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-6388        TCGA-06-6389        TCGA-06-6390        TCGA-06-6391 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-6693        TCGA-06-6694        TCGA-06-6695        TCGA-06-6697 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-6698        TCGA-06-6699        TCGA-06-6700        TCGA-06-6701 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-08-0245        TCGA-08-0344        TCGA-08-0345        TCGA-08-0346 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-08-0347        TCGA-08-0348        TCGA-08-0349        TCGA-08-0350 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-08-0351        TCGA-08-0352        TCGA-08-0353        TCGA-08-0354 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-08-0355        TCGA-08-0356        TCGA-08-0357        TCGA-08-0358 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-08-0359        TCGA-08-0375        TCGA-08-0380        TCGA-08-0386 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-08-0389        TCGA-08-0390        TCGA-08-0392        TCGA-12-0691 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-12-0692        TCGA-12-1598        TCGA-12-1599        TCGA-12-3646 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-12-3649        TCGA-12-3650        TCGA-12-3651        TCGA-12-3652 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-12-3653        TCGA-12-5295        TCGA-12-5301        TCGA-14-0813 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-14-0862        TCGA-14-0871        TCGA-15-1446        TCGA-15-1447 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-15-1449        TCGA-16-0846        TCGA-16-1460        TCGA-19-0957 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-0962        TCGA-19-1386        TCGA-19-1389        TCGA-19-1390 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-1392        TCGA-19-1786        TCGA-19-1789        TCGA-19-1791 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-2619        TCGA-19-2620        TCGA-19-2625        TCGA-19-2631 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-5947        TCGA-19-5950        TCGA-19-5951        TCGA-19-5952 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-5953        TCGA-19-5954        TCGA-19-5955        TCGA-19-5956 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-5958        TCGA-19-5959        TCGA-19-5960        TCGA-26-1440 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-26-6173        TCGA-26-6174        TCGA-27-1830        TCGA-27-1831 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-27-1832        TCGA-27-1833        TCGA-27-1834        TCGA-27-1836 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-27-2518        TCGA-27-2528        TCGA-28-1746        TCGA-28-1747 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-28-1750        TCGA-28-1752        TCGA-28-1753        TCGA-28-1757 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-28-2501        TCGA-28-5208        TCGA-28-5214        TCGA-32-1970 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-32-1976        TCGA-32-1978        TCGA-32-1982        TCGA-32-1986 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-32-1987        TCGA-32-1991        TCGA-32-4210        TCGA-32-4211 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-32-5222        TCGA-41-2573        TCGA-41-2575        TCGA-41-3392 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-41-3393        TCGA-41-3915        TCGA-41-4097        TCGA-41-5651 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4926 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-6192 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-6193        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-6656        TCGA-76-6657        TCGA-76-6660        TCGA-76-6662 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-6663        TCGA-76-6664        TCGA-81-5910 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
D10V8, multiclass
[1] "Remove cluster labels:" "5Q GAIN MUTATED"       
clus
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2               199 
       TCGA-02-0003        TCGA-02-0011        TCGA-02-0014        TCGA-02-0068 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-02-0069        TCGA-02-0116        TCGA-02-2470        TCGA-02-2485 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-0125        TCGA-06-0126        TCGA-06-0128        TCGA-06-0129 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-0130        TCGA-06-0154        TCGA-06-0155        TCGA-06-0171 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-0189        TCGA-06-0238        TCGA-06-0644        TCGA-06-0650 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-0875        TCGA-06-0876        TCGA-06-0877        TCGA-06-0878 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-0879        TCGA-06-0882        TCGA-06-0939        TCGA-06-1084 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-1086        TCGA-06-1087        TCGA-06-1800        TCGA-06-1802 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-1804        TCGA-06-1805        TCGA-06-2557        TCGA-06-2558 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-2559        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2566        TCGA-06-2567        TCGA-06-2570 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-5408        TCGA-06-5410        TCGA-06-5411        TCGA-06-5412 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-5413        TCGA-06-5414        TCGA-06-5415        TCGA-06-5416 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-5418        TCGA-06-5856        TCGA-06-5858        TCGA-06-5859 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-6388        TCGA-06-6389        TCGA-06-6390        TCGA-06-6391 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-6693        TCGA-06-6694        TCGA-06-6695        TCGA-06-6697 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-06-6698        TCGA-06-6699        TCGA-06-6700        TCGA-06-6701 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-08-0245        TCGA-08-0344        TCGA-08-0345        TCGA-08-0346 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-08-0347        TCGA-08-0348        TCGA-08-0349        TCGA-08-0350 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-08-0351        TCGA-08-0352        TCGA-08-0353        TCGA-08-0354 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-08-0355        TCGA-08-0356        TCGA-08-0357        TCGA-08-0358 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-08-0359        TCGA-08-0375        TCGA-08-0380        TCGA-08-0386 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-08-0389        TCGA-08-0390        TCGA-08-0392        TCGA-12-0691 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-12-0692        TCGA-12-1598        TCGA-12-1599        TCGA-12-3646 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-12-3649        TCGA-12-3650        TCGA-12-3651        TCGA-12-3652 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-12-3653        TCGA-12-5295        TCGA-12-5301        TCGA-14-0813 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-14-0862        TCGA-14-0871        TCGA-15-1446        TCGA-15-1447 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-15-1449        TCGA-16-0846        TCGA-16-1460        TCGA-19-0957 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-0962        TCGA-19-1386        TCGA-19-1389        TCGA-19-1390 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-1392        TCGA-19-1786        TCGA-19-1789        TCGA-19-1791 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-2619        TCGA-19-2620        TCGA-19-2625        TCGA-19-2631 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-5947        TCGA-19-5950        TCGA-19-5951        TCGA-19-5952 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-5953        TCGA-19-5954        TCGA-19-5955        TCGA-19-5956 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-19-5958        TCGA-19-5959        TCGA-19-5960        TCGA-26-1440 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-26-6173        TCGA-26-6174        TCGA-27-1830        TCGA-27-1831 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-27-1832        TCGA-27-1833        TCGA-27-1834        TCGA-27-1836 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-27-2518        TCGA-27-2528        TCGA-28-1746        TCGA-28-1747 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-28-1750        TCGA-28-1752        TCGA-28-1753        TCGA-28-1757 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-28-2501        TCGA-28-5208        TCGA-28-5214        TCGA-32-1970 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-32-1976        TCGA-32-1978        TCGA-32-1982        TCGA-32-1986 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-32-1987        TCGA-32-1991        TCGA-32-4210        TCGA-32-4211 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-32-5222        TCGA-41-2573        TCGA-41-2575        TCGA-41-3392 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-41-3393        TCGA-41-3915        TCGA-41-4097        TCGA-41-5651 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4926 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-6192 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-6193        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-6656        TCGA-76-6657        TCGA-76-6660        TCGA-76-6662 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-76-6663        TCGA-76-6664        TCGA-81-5910 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
D10V9, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1                43
  CLUS_2               4                63
  CLUS_3               0                36
D10V10, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               4                62
  CLUS_2               0                21
  CLUS_3               1                59

Clustering(11) Variable = 6p gain mutation analysis
D11V1, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2               170
  CLUS_2               3               167
  CLUS_3               1               166
D11V2, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2               215
  CLUS_2               1               125
  CLUS_3               3               163
D11V3, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1               138
  CLUS_2               3               154
  CLUS_3               0                72
  CLUS_4               2               102
D11V4, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2               161
  CLUS_2               1               178
  CLUS_3               3               127
D11V5, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1               160
  CLUS_2               1               213
  CLUS_3               5               183
D11V6, multiclass
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1               108 
       TCGA-06-0650        TCGA-06-1804        TCGA-06-1806        TCGA-06-5408 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-06-6388 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-6389        TCGA-06-6390        TCGA-06-6391        TCGA-06-6693 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-6694        TCGA-06-6695        TCGA-06-6697        TCGA-06-6698 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-6699        TCGA-06-6700        TCGA-06-6701        TCGA-12-5295 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-12-5299        TCGA-12-5301        TCGA-14-0740        TCGA-14-0781 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-14-0862        TCGA-14-1043        TCGA-14-1395        TCGA-14-1450 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-15-1444        TCGA-19-4065        TCGA-19-5947        TCGA-19-5950 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-5951        TCGA-19-5952        TCGA-19-5953        TCGA-19-5954 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-5955        TCGA-19-5956        TCGA-19-5958        TCGA-19-5959 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-5960        TCGA-26-1442        TCGA-26-5132        TCGA-26-5133 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-26-5134        TCGA-26-5135        TCGA-26-5136        TCGA-26-5139 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-26-6173        TCGA-26-6174        TCGA-28-2501        TCGA-28-2510 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-28-5204        TCGA-28-5207        TCGA-28-5208        TCGA-28-5209 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-28-5211        TCGA-28-5213        TCGA-28-5214        TCGA-28-5215 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-28-5216        TCGA-28-5218        TCGA-28-5219        TCGA-28-5220 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-28-6450        TCGA-32-1979        TCGA-32-1980        TCGA-32-5222 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-41-5651        TCGA-41-6646        TCGA-74-6573        TCGA-74-6575 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-74-6577        TCGA-74-6578        TCGA-74-6581        TCGA-74-6584 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-4925        TCGA-76-4926        TCGA-76-4928        TCGA-76-4929 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-4931        TCGA-76-4934        TCGA-76-4935        TCGA-76-6191 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-6192        TCGA-76-6193        TCGA-76-6280        TCGA-76-6282 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-6283        TCGA-76-6285        TCGA-76-6286        TCGA-76-6656 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-6657        TCGA-76-6660        TCGA-76-6661        TCGA-76-6662 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-6663        TCGA-76-6664        TCGA-81-5910        TCGA-87-5896 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
D11V7, multiclass
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                2               199 
       TCGA-02-0003        TCGA-02-0011        TCGA-02-0014        TCGA-02-0068 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-02-0116        TCGA-02-2470        TCGA-02-2485        TCGA-06-0125 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-0126        TCGA-06-0128        TCGA-06-0129        TCGA-06-0130 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-0154        TCGA-06-0155        TCGA-06-0171        TCGA-06-0189 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-0238        TCGA-06-0644        TCGA-06-0650        TCGA-06-0875 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-0876        TCGA-06-0877        TCGA-06-0878        TCGA-06-0879 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-0882        TCGA-06-0939        TCGA-06-1084        TCGA-06-1086 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-1087        TCGA-06-1800        TCGA-06-1802        TCGA-06-1804 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-1805        TCGA-06-1806        TCGA-06-2557        TCGA-06-2558 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-2559        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2566        TCGA-06-2567        TCGA-06-2570 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-5408        TCGA-06-5410        TCGA-06-5411        TCGA-06-5412 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-5413        TCGA-06-5414        TCGA-06-5415        TCGA-06-5416 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-5418        TCGA-06-5856        TCGA-06-5858        TCGA-06-5859 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-6388        TCGA-06-6389        TCGA-06-6390        TCGA-06-6391 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-6693        TCGA-06-6694        TCGA-06-6695        TCGA-06-6697 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-6698        TCGA-06-6699        TCGA-06-6700        TCGA-06-6701 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-08-0245        TCGA-08-0344        TCGA-08-0345        TCGA-08-0346 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-08-0347        TCGA-08-0348        TCGA-08-0349        TCGA-08-0350 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-08-0351        TCGA-08-0352        TCGA-08-0353        TCGA-08-0354 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-08-0355        TCGA-08-0356        TCGA-08-0357        TCGA-08-0358 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-08-0359        TCGA-08-0375        TCGA-08-0380        TCGA-08-0386 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-08-0389        TCGA-08-0390        TCGA-08-0392        TCGA-12-0691 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-12-0692        TCGA-12-1598        TCGA-12-1599        TCGA-12-3646 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-12-3649        TCGA-12-3650        TCGA-12-3651        TCGA-12-3652 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-12-3653        TCGA-12-5295        TCGA-12-5301        TCGA-14-0813 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-14-0862        TCGA-14-0871        TCGA-14-1823        TCGA-15-1446 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-15-1449        TCGA-16-0846        TCGA-16-1460        TCGA-19-0957 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-0962        TCGA-19-1386        TCGA-19-1389        TCGA-19-1390 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-1392        TCGA-19-1786        TCGA-19-1789        TCGA-19-1791 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-2619        TCGA-19-2620        TCGA-19-2625        TCGA-19-2631 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-5947        TCGA-19-5950        TCGA-19-5951        TCGA-19-5952 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-5953        TCGA-19-5954        TCGA-19-5955        TCGA-19-5956 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-5958        TCGA-19-5959        TCGA-19-5960        TCGA-26-1440 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-26-6173        TCGA-26-6174        TCGA-27-1830        TCGA-27-1831 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-27-1832        TCGA-27-1833        TCGA-27-1834        TCGA-27-1836 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-27-2518        TCGA-27-2528        TCGA-28-1746        TCGA-28-1747 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-28-1750        TCGA-28-1752        TCGA-28-1753        TCGA-28-1757 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-28-2501        TCGA-28-5208        TCGA-28-5214        TCGA-32-1970 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-32-1976        TCGA-32-1978        TCGA-32-1982        TCGA-32-1986 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-32-1987        TCGA-32-1991        TCGA-32-4210        TCGA-32-4211 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-32-5222        TCGA-41-2573        TCGA-41-2575        TCGA-41-3392 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-41-3393        TCGA-41-3915        TCGA-41-4097        TCGA-41-5651 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4926 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-6192 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-6193        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-6656        TCGA-76-6657        TCGA-76-6660        TCGA-76-6662 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-6663        TCGA-76-6664        TCGA-81-5910 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
D11V8, multiclass
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                2               199 
       TCGA-02-0003        TCGA-02-0011        TCGA-02-0014        TCGA-02-0068 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-02-0116        TCGA-02-2470        TCGA-02-2485        TCGA-06-0125 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-0126        TCGA-06-0128        TCGA-06-0129        TCGA-06-0130 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-0154        TCGA-06-0155        TCGA-06-0171        TCGA-06-0189 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-0238        TCGA-06-0644        TCGA-06-0650        TCGA-06-0875 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-0876        TCGA-06-0877        TCGA-06-0878        TCGA-06-0879 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-0882        TCGA-06-0939        TCGA-06-1084        TCGA-06-1086 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-1087        TCGA-06-1800        TCGA-06-1802        TCGA-06-1804 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-1805        TCGA-06-1806        TCGA-06-2557        TCGA-06-2558 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-2559        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2566        TCGA-06-2567        TCGA-06-2570 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-5408        TCGA-06-5410        TCGA-06-5411        TCGA-06-5412 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-5413        TCGA-06-5414        TCGA-06-5415        TCGA-06-5416 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-5418        TCGA-06-5856        TCGA-06-5858        TCGA-06-5859 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-6388        TCGA-06-6389        TCGA-06-6390        TCGA-06-6391 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-6693        TCGA-06-6694        TCGA-06-6695        TCGA-06-6697 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-06-6698        TCGA-06-6699        TCGA-06-6700        TCGA-06-6701 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-08-0245        TCGA-08-0344        TCGA-08-0345        TCGA-08-0346 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-08-0347        TCGA-08-0348        TCGA-08-0349        TCGA-08-0350 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-08-0351        TCGA-08-0352        TCGA-08-0353        TCGA-08-0354 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-08-0355        TCGA-08-0356        TCGA-08-0357        TCGA-08-0358 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-08-0359        TCGA-08-0375        TCGA-08-0380        TCGA-08-0386 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-08-0389        TCGA-08-0390        TCGA-08-0392        TCGA-12-0691 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-12-0692        TCGA-12-1598        TCGA-12-1599        TCGA-12-3646 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-12-3649        TCGA-12-3650        TCGA-12-3651        TCGA-12-3652 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-12-3653        TCGA-12-5295        TCGA-12-5301        TCGA-14-0813 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-14-0862        TCGA-14-0871        TCGA-14-1823        TCGA-15-1446 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-15-1449        TCGA-16-0846        TCGA-16-1460        TCGA-19-0957 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-0962        TCGA-19-1386        TCGA-19-1389        TCGA-19-1390 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-1392        TCGA-19-1786        TCGA-19-1789        TCGA-19-1791 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-2619        TCGA-19-2620        TCGA-19-2625        TCGA-19-2631 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-5947        TCGA-19-5950        TCGA-19-5951        TCGA-19-5952 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-5953        TCGA-19-5954        TCGA-19-5955        TCGA-19-5956 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-19-5958        TCGA-19-5959        TCGA-19-5960        TCGA-26-1440 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-26-6173        TCGA-26-6174        TCGA-27-1830        TCGA-27-1831 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-27-1832        TCGA-27-1833        TCGA-27-1834        TCGA-27-1836 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-27-2518        TCGA-27-2528        TCGA-28-1746        TCGA-28-1747 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-28-1750        TCGA-28-1752        TCGA-28-1753        TCGA-28-1757 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-28-2501        TCGA-28-5208        TCGA-28-5214        TCGA-32-1970 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-32-1976        TCGA-32-1978        TCGA-32-1982        TCGA-32-1986 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-32-1987        TCGA-32-1991        TCGA-32-4210        TCGA-32-4211 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-32-5222        TCGA-41-2573        TCGA-41-2575        TCGA-41-3392 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-41-3393        TCGA-41-3915        TCGA-41-4097        TCGA-41-5651 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4926 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-6192 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-6193        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-6656        TCGA-76-6657        TCGA-76-6660        TCGA-76-6662 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-76-6663        TCGA-76-6664        TCGA-81-5910 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
D11V9, multiclass
D11V10, multiclass

Clustering(12) Variable = 6q gain mutation analysis
D12V1, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               2               170
  CLUS_2               5               165
  CLUS_3               1               166
D12V2, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               3               214
  CLUS_2               1               125
  CLUS_3               4               162
D12V3, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               2               137
  CLUS_2               3               154
  CLUS_3               0                72
  CLUS_4               3               101
D12V4, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               3               160
  CLUS_2               2               177
  CLUS_3               3               127
D12V5, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               1               160
  CLUS_2               1               213
  CLUS_3               7               181
D12V6, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                1               108 
       TCGA-06-0650        TCGA-06-1804        TCGA-06-1806        TCGA-06-5408 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-06-6388 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-6389        TCGA-06-6390        TCGA-06-6391        TCGA-06-6693 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-6694        TCGA-06-6695        TCGA-06-6697        TCGA-06-6698 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-6699        TCGA-06-6700        TCGA-06-6701        TCGA-12-5295 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-5299        TCGA-12-5301        TCGA-14-0740        TCGA-14-0781 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-14-0862        TCGA-14-1043        TCGA-14-1395        TCGA-14-1450 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-15-1444        TCGA-19-4065        TCGA-19-5947        TCGA-19-5950 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-5951        TCGA-19-5952        TCGA-19-5953        TCGA-19-5954 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-5955        TCGA-19-5956        TCGA-19-5958        TCGA-19-5959 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-5960        TCGA-26-1442        TCGA-26-5132        TCGA-26-5133 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-26-5134        TCGA-26-5135        TCGA-26-5136        TCGA-26-5139 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-26-6173        TCGA-26-6174        TCGA-28-2501        TCGA-28-2510 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-5204        TCGA-28-5207        TCGA-28-5208        TCGA-28-5209 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-5211        TCGA-28-5213        TCGA-28-5214        TCGA-28-5215 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-5216        TCGA-28-5218        TCGA-28-5219        TCGA-28-5220 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-6450        TCGA-32-1979        TCGA-32-1980        TCGA-32-5222 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-41-5651        TCGA-41-6646        TCGA-74-6573        TCGA-74-6575 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-74-6577        TCGA-74-6578        TCGA-74-6581        TCGA-74-6584 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-4925        TCGA-76-4926        TCGA-76-4928        TCGA-76-4929 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-4931        TCGA-76-4934        TCGA-76-4935        TCGA-76-6191 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-6192        TCGA-76-6193        TCGA-76-6280        TCGA-76-6282 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-6283        TCGA-76-6285        TCGA-76-6286        TCGA-76-6656 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-6657        TCGA-76-6660        TCGA-76-6661        TCGA-76-6662 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-6663        TCGA-76-6664        TCGA-81-5910        TCGA-87-5896 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D12V7, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2               199 
       TCGA-02-0003        TCGA-02-0011        TCGA-02-0014        TCGA-02-0068 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-02-0116        TCGA-02-2470        TCGA-02-2485        TCGA-06-0125 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0126        TCGA-06-0128        TCGA-06-0129        TCGA-06-0130 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0154        TCGA-06-0155        TCGA-06-0171        TCGA-06-0189 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0238        TCGA-06-0644        TCGA-06-0650        TCGA-06-0875 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0876        TCGA-06-0877        TCGA-06-0878        TCGA-06-0879 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0882        TCGA-06-0939        TCGA-06-1084        TCGA-06-1086 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-1087        TCGA-06-1800        TCGA-06-1802        TCGA-06-1804 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-1805        TCGA-06-1806        TCGA-06-2557        TCGA-06-2558 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-2559        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2566        TCGA-06-2567        TCGA-06-2570 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5408        TCGA-06-5410        TCGA-06-5411        TCGA-06-5412 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5413        TCGA-06-5414        TCGA-06-5415        TCGA-06-5416 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5418        TCGA-06-5856        TCGA-06-5858        TCGA-06-5859 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-6388        TCGA-06-6389        TCGA-06-6390        TCGA-06-6391 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-6693        TCGA-06-6694        TCGA-06-6695        TCGA-06-6697 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-6698        TCGA-06-6699        TCGA-06-6700        TCGA-06-6701 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-08-0245        TCGA-08-0344        TCGA-08-0345        TCGA-08-0346 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-08-0347        TCGA-08-0348        TCGA-08-0349        TCGA-08-0350 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-08-0351        TCGA-08-0352        TCGA-08-0353        TCGA-08-0354 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-08-0355        TCGA-08-0356        TCGA-08-0357        TCGA-08-0358 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-08-0359        TCGA-08-0375        TCGA-08-0380        TCGA-08-0386 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-08-0389        TCGA-08-0390        TCGA-08-0392        TCGA-12-0691 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-0692        TCGA-12-1598        TCGA-12-1599        TCGA-12-3646 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-3649        TCGA-12-3650        TCGA-12-3651        TCGA-12-3652 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-3653        TCGA-12-5295        TCGA-12-5301        TCGA-14-0813 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-14-0862        TCGA-14-0871        TCGA-14-1823        TCGA-15-1446 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-15-1449        TCGA-16-0846        TCGA-16-1460        TCGA-19-0957 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-0962        TCGA-19-1386        TCGA-19-1389        TCGA-19-1390 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-1392        TCGA-19-1786        TCGA-19-1789        TCGA-19-1791 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-2619        TCGA-19-2620        TCGA-19-2625        TCGA-19-2631 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-5947        TCGA-19-5950        TCGA-19-5951        TCGA-19-5952 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-5953        TCGA-19-5954        TCGA-19-5955        TCGA-19-5956 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-5958        TCGA-19-5959        TCGA-19-5960        TCGA-26-1440 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-26-6173        TCGA-26-6174        TCGA-27-1830        TCGA-27-1831 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-27-1832        TCGA-27-1833        TCGA-27-1834        TCGA-27-1836 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-27-2518        TCGA-27-2528        TCGA-28-1746        TCGA-28-1747 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-1750        TCGA-28-1752        TCGA-28-1753        TCGA-28-1757 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-2501        TCGA-28-5208        TCGA-28-5214        TCGA-32-1970 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-32-1976        TCGA-32-1978        TCGA-32-1982        TCGA-32-1986 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-32-1987        TCGA-32-1991        TCGA-32-4210        TCGA-32-4211 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-32-5222        TCGA-41-2573        TCGA-41-2575        TCGA-41-3392 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-41-3393        TCGA-41-3915        TCGA-41-4097        TCGA-41-5651 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4926 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-6192 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-6193        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-6656        TCGA-76-6657        TCGA-76-6660        TCGA-76-6662 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-6663        TCGA-76-6664        TCGA-81-5910 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D12V8, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2               199 
       TCGA-02-0003        TCGA-02-0011        TCGA-02-0014        TCGA-02-0068 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-02-0116        TCGA-02-2470        TCGA-02-2485        TCGA-06-0125 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0126        TCGA-06-0128        TCGA-06-0129        TCGA-06-0130 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0154        TCGA-06-0155        TCGA-06-0171        TCGA-06-0189 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0238        TCGA-06-0644        TCGA-06-0650        TCGA-06-0875 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0876        TCGA-06-0877        TCGA-06-0878        TCGA-06-0879 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0882        TCGA-06-0939        TCGA-06-1084        TCGA-06-1086 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-1087        TCGA-06-1800        TCGA-06-1802        TCGA-06-1804 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-1805        TCGA-06-1806        TCGA-06-2557        TCGA-06-2558 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-2559        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2566        TCGA-06-2567        TCGA-06-2570 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5408        TCGA-06-5410        TCGA-06-5411        TCGA-06-5412 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5413        TCGA-06-5414        TCGA-06-5415        TCGA-06-5416 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5418        TCGA-06-5856        TCGA-06-5858        TCGA-06-5859 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-6388        TCGA-06-6389        TCGA-06-6390        TCGA-06-6391 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-6693        TCGA-06-6694        TCGA-06-6695        TCGA-06-6697 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-6698        TCGA-06-6699        TCGA-06-6700        TCGA-06-6701 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-08-0245        TCGA-08-0344        TCGA-08-0345        TCGA-08-0346 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-08-0347        TCGA-08-0348        TCGA-08-0349        TCGA-08-0350 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-08-0351        TCGA-08-0352        TCGA-08-0353        TCGA-08-0354 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-08-0355        TCGA-08-0356        TCGA-08-0357        TCGA-08-0358 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-08-0359        TCGA-08-0375        TCGA-08-0380        TCGA-08-0386 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-08-0389        TCGA-08-0390        TCGA-08-0392        TCGA-12-0691 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-0692        TCGA-12-1598        TCGA-12-1599        TCGA-12-3646 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-3649        TCGA-12-3650        TCGA-12-3651        TCGA-12-3652 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-3653        TCGA-12-5295        TCGA-12-5301        TCGA-14-0813 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-14-0862        TCGA-14-0871        TCGA-14-1823        TCGA-15-1446 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-15-1449        TCGA-16-0846        TCGA-16-1460        TCGA-19-0957 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-0962        TCGA-19-1386        TCGA-19-1389        TCGA-19-1390 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-1392        TCGA-19-1786        TCGA-19-1789        TCGA-19-1791 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-2619        TCGA-19-2620        TCGA-19-2625        TCGA-19-2631 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-5947        TCGA-19-5950        TCGA-19-5951        TCGA-19-5952 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-5953        TCGA-19-5954        TCGA-19-5955        TCGA-19-5956 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-5958        TCGA-19-5959        TCGA-19-5960        TCGA-26-1440 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-26-6173        TCGA-26-6174        TCGA-27-1830        TCGA-27-1831 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-27-1832        TCGA-27-1833        TCGA-27-1834        TCGA-27-1836 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-27-2518        TCGA-27-2528        TCGA-28-1746        TCGA-28-1747 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-1750        TCGA-28-1752        TCGA-28-1753        TCGA-28-1757 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-2501        TCGA-28-5208        TCGA-28-5214        TCGA-32-1970 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-32-1976        TCGA-32-1978        TCGA-32-1982        TCGA-32-1986 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-32-1987        TCGA-32-1991        TCGA-32-4210        TCGA-32-4211 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-32-5222        TCGA-41-2573        TCGA-41-2575        TCGA-41-3392 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-41-3393        TCGA-41-3915        TCGA-41-4097        TCGA-41-5651 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4926 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-6192 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-6193        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-6656        TCGA-76-6657        TCGA-76-6660        TCGA-76-6662 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-6663        TCGA-76-6664        TCGA-81-5910 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D12V9, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                1               146 
       TCGA-02-0047        TCGA-02-0055        TCGA-02-2483        TCGA-02-2485 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-02-2486        TCGA-06-0125        TCGA-06-0129        TCGA-06-0130 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0132        TCGA-06-0138        TCGA-06-0141        TCGA-06-0157 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0158        TCGA-06-0168        TCGA-06-0174        TCGA-06-0178 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0184        TCGA-06-0187        TCGA-06-0190        TCGA-06-0210 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0211        TCGA-06-0219        TCGA-06-0238        TCGA-06-0644 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0645        TCGA-06-0646        TCGA-06-0649        TCGA-06-0686 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0743        TCGA-06-0744        TCGA-06-0745        TCGA-06-0747 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0749        TCGA-06-0750        TCGA-06-0878        TCGA-06-0882 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-1804        TCGA-06-2557        TCGA-06-2558        TCGA-06-2559 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-2561        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2567        TCGA-06-2570        TCGA-06-5408 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-08-0386 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-0616        TCGA-12-0618        TCGA-12-0619        TCGA-12-0821 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-3650        TCGA-12-3652        TCGA-12-3653        TCGA-12-5295 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-5299        TCGA-14-0781        TCGA-14-0787        TCGA-14-0789 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-14-0790        TCGA-14-0817        TCGA-14-1034        TCGA-14-1823 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-14-1825        TCGA-14-1829        TCGA-14-2554        TCGA-15-0742 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-15-1444        TCGA-16-0846        TCGA-16-1045        TCGA-19-1390 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-1787        TCGA-19-2619        TCGA-19-2620        TCGA-19-2624 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-2625        TCGA-19-2629        TCGA-19-4065        TCGA-19-5960 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-27-1830 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-27-1831        TCGA-27-1832        TCGA-27-1834        TCGA-27-1835 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-27-1837        TCGA-27-2519        TCGA-27-2521        TCGA-27-2523 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-27-2524        TCGA-27-2526        TCGA-27-2528        TCGA-28-1747 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-1753        TCGA-28-2509        TCGA-28-2510        TCGA-28-2513 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-2514        TCGA-28-5204        TCGA-28-5207        TCGA-28-5208 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-5209        TCGA-28-5213        TCGA-28-5215        TCGA-28-5216 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5220        TCGA-32-1970        TCGA-32-1980 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-32-1982        TCGA-32-2615        TCGA-32-2616        TCGA-32-2632 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-32-2634        TCGA-32-2638        TCGA-32-4213        TCGA-32-5222 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-41-2571        TCGA-41-2572        TCGA-41-3915        TCGA-41-4097 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-41-5651        TCGA-76-4925        TCGA-76-4926        TCGA-76-4928 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-4929        TCGA-76-4931 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D12V10, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                1               146 
       TCGA-02-0047        TCGA-02-0055        TCGA-02-2483        TCGA-02-2485 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-02-2486        TCGA-06-0125        TCGA-06-0129        TCGA-06-0130 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0132        TCGA-06-0138        TCGA-06-0141        TCGA-06-0157 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0158        TCGA-06-0168        TCGA-06-0174        TCGA-06-0178 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0184        TCGA-06-0187        TCGA-06-0190        TCGA-06-0210 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0211        TCGA-06-0219        TCGA-06-0238        TCGA-06-0644 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0645        TCGA-06-0646        TCGA-06-0649        TCGA-06-0686 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0743        TCGA-06-0744        TCGA-06-0745        TCGA-06-0747 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-0749        TCGA-06-0750        TCGA-06-0878        TCGA-06-0882 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-1804        TCGA-06-2557        TCGA-06-2558        TCGA-06-2559 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-2561        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2567        TCGA-06-2570        TCGA-06-5408 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-08-0386 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-0616        TCGA-12-0618        TCGA-12-0619        TCGA-12-0821 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-3650        TCGA-12-3652        TCGA-12-3653        TCGA-12-5295 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-12-5299        TCGA-14-0781        TCGA-14-0787        TCGA-14-0789 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-14-0790        TCGA-14-0817        TCGA-14-1034        TCGA-14-1823 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-14-1825        TCGA-14-1829        TCGA-14-2554        TCGA-15-0742 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-15-1444        TCGA-16-0846        TCGA-16-1045        TCGA-19-1390 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-1787        TCGA-19-2619        TCGA-19-2620        TCGA-19-2624 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-19-2625        TCGA-19-2629        TCGA-19-4065        TCGA-19-5960 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-27-1830 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-27-1831        TCGA-27-1832        TCGA-27-1834        TCGA-27-1835 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-27-1837        TCGA-27-2519        TCGA-27-2521        TCGA-27-2523 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-27-2524        TCGA-27-2526        TCGA-27-2528        TCGA-28-1747 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-1753        TCGA-28-2509        TCGA-28-2510        TCGA-28-2513 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-2514        TCGA-28-5204        TCGA-28-5207        TCGA-28-5208 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-5209        TCGA-28-5213        TCGA-28-5215        TCGA-28-5216 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5220        TCGA-32-1970        TCGA-32-1980 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-32-1982        TCGA-32-2615        TCGA-32-2616        TCGA-32-2632 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-32-2634        TCGA-32-2638        TCGA-32-4213        TCGA-32-5222 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-41-2571        TCGA-41-2572        TCGA-41-3915        TCGA-41-4097 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-41-5651        TCGA-76-4925        TCGA-76-4926        TCGA-76-4928 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-76-4929        TCGA-76-4931 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 

Clustering(13) Variable = 7p gain mutation analysis
D13V1, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1             141                31
  CLUS_2             104                66
  CLUS_3             145                22
D13V2, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1             179                38
  CLUS_2             108                18
  CLUS_3             103                63
D13V3, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1             120                19
  CLUS_2             112                45
  CLUS_3              48                24
  CLUS_4              87                17
D13V4, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1             135                28
  CLUS_2             157                22
  CLUS_3              75                55
D13V5, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1             140                21
  CLUS_2             190                24
  CLUS_3             104                84
D13V6, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              28                10
  CLUS_2              20                 0
  CLUS_3              21                 3
  CLUS_4              15                12
D13V7, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              40                14
  CLUS_2              39                19
  CLUS_3              37                 7
  CLUS_4              43                 2
D13V8, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              54                10
  CLUS_2              25                 8
  CLUS_3              80                24
D13V9, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              28                16
  CLUS_2              56                11
  CLUS_3              25                11
D13V10, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              56                10
  CLUS_2              17                 4
  CLUS_3              36                24

Clustering(14) Variable = 7q gain mutation analysis
D14V1, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1             140                32
  CLUS_2             109                61
  CLUS_3             144                23
D14V2, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1             179                38
  CLUS_2             107                19
  CLUS_3             107                59
D14V3, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1             121                18
  CLUS_2             111                46
  CLUS_3              50                22
  CLUS_4              86                18
D14V4, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1             135                28
  CLUS_2             153                26
  CLUS_3              80                50
D14V5, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1             137                24
  CLUS_2             193                21
  CLUS_3             109                79
D14V6, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              30                 8
  CLUS_2              19                 1
  CLUS_3              22                 2
  CLUS_4              15                12
D14V7, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              39                15
  CLUS_2              42                16
  CLUS_3              39                 5
  CLUS_4              41                 4
D14V8, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              55                 9
  CLUS_2              26                 7
  CLUS_3              80                24
D14V9, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              28                16
  CLUS_2              55                12
  CLUS_3              28                 8
D14V10, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              57                 9
  CLUS_2              16                 5
  CLUS_3              38                22

Clustering(15) Variable = 8p gain mutation analysis
D15V1, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               6               166
  CLUS_2              16               154
  CLUS_3               2               165
D15V2, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              10               207
  CLUS_2               2               124
  CLUS_3              12               154
D15V3, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               4               135
  CLUS_2               8               149
  CLUS_3               6                66
  CLUS_4               4               100
D15V4, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               7               156
  CLUS_2               3               176
  CLUS_3              12               118
D15V5, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              15               146
  CLUS_2               3               211
  CLUS_3               8               180
D15V6, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                37
  CLUS_2               0                20
  CLUS_3               0                24
  CLUS_4               3                24
D15V7, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                53
  CLUS_2               7                51
  CLUS_3               1                43
  CLUS_4               1                44
D15V8, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                63
  CLUS_2               0                33
  CLUS_3               9                95
D15V9, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               3                41
  CLUS_2               4                63
  CLUS_3               1                35
D15V10, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               5                61
  CLUS_2               0                21
  CLUS_3               3                57

Clustering(16) Variable = 8q gain mutation analysis
D16V1, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               6               166
  CLUS_2              19               151
  CLUS_3               3               164
D16V2, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              10               207
  CLUS_2               3               123
  CLUS_3              15               151
D16V3, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               5               134
  CLUS_2              13               144
  CLUS_3               5                67
  CLUS_4               4               100
D16V4, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               7               156
  CLUS_2               5               174
  CLUS_3              15               115
D16V5, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              15               146
  CLUS_2               4               210
  CLUS_3              12               176
D16V6, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1                37
  CLUS_2               0                20
  CLUS_3               0                24
  CLUS_4               4                23
D16V7, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1                53
  CLUS_2               7                51
  CLUS_3               1                43
  CLUS_4               1                44
D16V8, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1                63
  CLUS_2               0                33
  CLUS_3               9                95
D16V9, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               5                39
  CLUS_2               4                63
  CLUS_3               1                35
D16V10, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               5                61
  CLUS_2               0                21
  CLUS_3               5                55

Clustering(17) Variable = 9p gain mutation analysis
D17V1, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               6               166
  CLUS_2               7               163
  CLUS_3               2               165
D17V2, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               8               209
  CLUS_2               0               126
  CLUS_3               7               159
D17V3, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               3               136
  CLUS_2               7               150
  CLUS_3               2                70
  CLUS_4               4               100
D17V4, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               4               159
  CLUS_2               6               173
  CLUS_3               6               124
D17V5, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               8               153
  CLUS_2               2               212
  CLUS_3               7               181
D17V6, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2                36
  CLUS_2               0                20
  CLUS_3               0                24
  CLUS_4               2                25
D17V7, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               3                51
  CLUS_2               2                56
  CLUS_3               0                44
  CLUS_4               0                45
D17V8, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               0                64
  CLUS_2               1                32
  CLUS_3               4               100
D17V9, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               3                41
  CLUS_2               4                63
  CLUS_3               0                36
D17V10, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               4                62
  CLUS_2               0                21
  CLUS_3               3                57

Clustering(18) Variable = 9q gain mutation analysis
D18V1, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1              11               161
  CLUS_2              13               157
  CLUS_3               7               160
D18V2, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1              16               201
  CLUS_2               2               124
  CLUS_3              13               153
D18V3, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               7               132
  CLUS_2              14               143
  CLUS_3               4                68
  CLUS_4               7                97
D18V4, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               9               154
  CLUS_2              13               166
  CLUS_3              10               120
D18V5, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1              13               148
  CLUS_2               8               206
  CLUS_3              13               175
D18V6, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2                36
  CLUS_2               1                19
  CLUS_3               1                23
  CLUS_4               1                26
D18V7, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               3                51
  CLUS_2               3                55
  CLUS_3               0                44
  CLUS_4               1                44
D18V8, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               0                64
  CLUS_2               2                31
  CLUS_3               5                99
D18V9, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               4                40
  CLUS_2               5                62
  CLUS_3               1                35
D18V10, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               5                61
  CLUS_2               2                19
  CLUS_3               3                57

Clustering(19) Variable = 10p gain mutation analysis
D19V1, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                2                170
  CLUS_2               10                160
  CLUS_3                0                167
D19V2, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                3                214
  CLUS_2                0                126
  CLUS_3                9                157
D19V3, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                138
  CLUS_2                7                150
  CLUS_3                3                 69
  CLUS_4                1                103
D19V4, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                162
  CLUS_2                2                177
  CLUS_3                9                121
D19V5, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                3                158
  CLUS_2                0                214
  CLUS_3                9                179
D19V6, multiclass
D19V7, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                 53
  CLUS_2                3                 55
  CLUS_3                0                 44
  CLUS_4                0                 45
D19V8, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                0                 64
  CLUS_2                1                 32
  CLUS_3                3                101
D19V9, multiclass
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                146 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2570         TCGA-06-5408 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-5410         TCGA-06-5411         TCGA-06-5412 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-5413         TCGA-06-5414         TCGA-06-5415 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-5416         TCGA-06-5418         TCGA-06-5856 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-5858         TCGA-06-5859         TCGA-08-0386 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-12-0616         TCGA-12-0618         TCGA-12-0619 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-12-0821         TCGA-12-3650         TCGA-12-3652 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-12-3653         TCGA-12-5295         TCGA-12-5299 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-14-0781         TCGA-14-0787         TCGA-14-0789 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-14-0790         TCGA-14-0817         TCGA-14-1034 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-14-1823         TCGA-14-1825         TCGA-14-1829 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-14-2554         TCGA-15-0742         TCGA-15-1444 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-16-0846         TCGA-16-1045         TCGA-19-1390 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2620 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-19-2624         TCGA-19-2625         TCGA-19-2629 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-19-4065         TCGA-19-5960         TCGA-26-1442 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-26-5135         TCGA-26-5136         TCGA-26-5139 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-27-1830         TCGA-27-1831         TCGA-27-1832 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1835         TCGA-27-1837 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-27-2519         TCGA-27-2521         TCGA-27-2523 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-27-2524         TCGA-27-2526         TCGA-27-2528 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-28-1747         TCGA-28-1753         TCGA-28-2509 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-28-2510         TCGA-28-2513         TCGA-28-2514 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5213         TCGA-28-5215 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-28-5216         TCGA-28-5218         TCGA-28-5220 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-32-1970         TCGA-32-1980         TCGA-32-1982 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-32-2615         TCGA-32-2616         TCGA-32-2632 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-32-2634         TCGA-32-2638         TCGA-32-4213 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-32-5222         TCGA-41-2571         TCGA-41-2572 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-41-3915         TCGA-41-4097         TCGA-41-5651 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-76-4925         TCGA-76-4926         TCGA-76-4928 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
D19V10, multiclass
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                146 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2570         TCGA-06-5408 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-5410         TCGA-06-5411         TCGA-06-5412 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-5413         TCGA-06-5414         TCGA-06-5415 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-5416         TCGA-06-5418         TCGA-06-5856 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-06-5858         TCGA-06-5859         TCGA-08-0386 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-12-0616         TCGA-12-0618         TCGA-12-0619 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-12-0821         TCGA-12-3650         TCGA-12-3652 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-12-3653         TCGA-12-5295         TCGA-12-5299 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-14-0781         TCGA-14-0787         TCGA-14-0789 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-14-0790         TCGA-14-0817         TCGA-14-1034 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-14-1823         TCGA-14-1825         TCGA-14-1829 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-14-2554         TCGA-15-0742         TCGA-15-1444 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-16-0846         TCGA-16-1045         TCGA-19-1390 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2620 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-19-2624         TCGA-19-2625         TCGA-19-2629 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-19-4065         TCGA-19-5960         TCGA-26-1442 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-26-5135         TCGA-26-5136         TCGA-26-5139 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-27-1830         TCGA-27-1831         TCGA-27-1832 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1835         TCGA-27-1837 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-27-2519         TCGA-27-2521         TCGA-27-2523 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-27-2524         TCGA-27-2526         TCGA-27-2528 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-28-1747         TCGA-28-1753         TCGA-28-2509 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-28-2510         TCGA-28-2513         TCGA-28-2514 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5213         TCGA-28-5215 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-28-5216         TCGA-28-5218         TCGA-28-5220 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-32-1970         TCGA-32-1980         TCGA-32-1982 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-32-2615         TCGA-32-2616         TCGA-32-2632 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-32-2634         TCGA-32-2638         TCGA-32-4213 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-32-5222         TCGA-41-2571         TCGA-41-2572 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-41-3915         TCGA-41-4097         TCGA-41-5651 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-76-4925         TCGA-76-4926         TCGA-76-4928 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 

Clustering(20) Variable = 11p gain mutation analysis
D20V1, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                171
  CLUS_2                1                169
  CLUS_3                1                166
D20V2, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                216
  CLUS_2                1                125
  CLUS_3                1                165
D20V3, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                2                137
  CLUS_2                1                156
  CLUS_3                0                 72
  CLUS_4                0                104
D20V4, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                163
  CLUS_2                2                177
  CLUS_3                1                129
D20V5, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                161
  CLUS_2                1                213
  CLUS_3                3                185
D20V6, multiclass
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                108 
        TCGA-06-0650         TCGA-06-1804         TCGA-06-1806 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5299         TCGA-12-5301 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-14-0740         TCGA-14-0781         TCGA-14-0862 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-14-1043         TCGA-14-1395         TCGA-14-1450 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-15-1444         TCGA-19-5947         TCGA-19-5950 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-5951         TCGA-19-5952         TCGA-19-5953 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-5954         TCGA-19-5955         TCGA-19-5956 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-5958         TCGA-19-5959         TCGA-19-5960 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-26-1442         TCGA-26-5132         TCGA-26-5133 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-26-5134         TCGA-26-5135         TCGA-26-5136 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-26-5139         TCGA-26-6173         TCGA-26-6174 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-2501         TCGA-28-2510         TCGA-28-5204 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-5211         TCGA-28-5213         TCGA-28-5214 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-5215         TCGA-28-5216         TCGA-28-5218 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-5219         TCGA-28-5220         TCGA-28-6450 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-1979         TCGA-32-1980         TCGA-32-5222 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-41-5651         TCGA-41-6646         TCGA-74-6573 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-74-6575         TCGA-74-6577         TCGA-74-6578 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-74-6581         TCGA-74-6584         TCGA-76-4925 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-4931         TCGA-76-4934         TCGA-76-4935 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6191         TCGA-76-6192         TCGA-76-6193 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6280         TCGA-76-6282         TCGA-76-6283 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6285         TCGA-76-6286         TCGA-76-6656 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6657         TCGA-76-6660         TCGA-76-6661 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6662         TCGA-76-6663         TCGA-76-6664 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-81-5910         TCGA-81-5911         TCGA-87-5896 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D20V7, multiclass
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                200 
        TCGA-02-0003         TCGA-02-0011         TCGA-02-0068 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-02-0069         TCGA-02-0116         TCGA-02-2470 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-06-0125         TCGA-06-0126 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0128         TCGA-06-0129         TCGA-06-0130 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0154         TCGA-06-0155         TCGA-06-0171 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0189         TCGA-06-0238         TCGA-06-0644 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0650         TCGA-06-0875         TCGA-06-0876 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0877         TCGA-06-0878         TCGA-06-0879 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0882         TCGA-06-0939         TCGA-06-1084 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-1086         TCGA-06-1087         TCGA-06-1800 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-1802         TCGA-06-1804         TCGA-06-1805 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-1806         TCGA-06-2557         TCGA-06-2558 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2562         TCGA-06-2563 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-2564         TCGA-06-2565         TCGA-06-2566 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2570         TCGA-06-5408 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5410         TCGA-06-5411         TCGA-06-5412 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5413         TCGA-06-5414         TCGA-06-5415 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5416         TCGA-06-5418         TCGA-06-5856 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5858         TCGA-06-5859         TCGA-06-6388 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-6389         TCGA-06-6390         TCGA-06-6391 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-6693         TCGA-06-6694         TCGA-06-6695 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-6697         TCGA-06-6698         TCGA-06-6699 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-6700         TCGA-06-6701         TCGA-08-0245 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0344         TCGA-08-0345         TCGA-08-0346 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0347         TCGA-08-0348         TCGA-08-0349 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0350         TCGA-08-0351         TCGA-08-0352 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0353         TCGA-08-0354         TCGA-08-0355 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0356         TCGA-08-0357         TCGA-08-0358 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0359         TCGA-08-0375         TCGA-08-0380 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0386         TCGA-08-0389         TCGA-08-0390 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0392         TCGA-12-0691         TCGA-12-0692 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-1598         TCGA-12-1599         TCGA-12-3646 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-3649         TCGA-12-3650         TCGA-12-3651 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-5301         TCGA-14-0813         TCGA-14-0862 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-14-0871         TCGA-14-1823         TCGA-15-1446 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-15-1447         TCGA-15-1449         TCGA-16-0846 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-16-1460         TCGA-19-0957         TCGA-19-0962 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-1386         TCGA-19-1389         TCGA-19-1390 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-1392         TCGA-19-1786         TCGA-19-1789 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-1791         TCGA-19-2619         TCGA-19-2620 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-2625         TCGA-19-2631         TCGA-19-5947 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-5950         TCGA-19-5951         TCGA-19-5952 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-5953         TCGA-19-5954         TCGA-19-5955 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-5956         TCGA-19-5958         TCGA-19-5959 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1440         TCGA-26-1442 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-26-6173         TCGA-26-6174         TCGA-27-1830 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1833 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1836         TCGA-27-2518 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-2528         TCGA-28-1746         TCGA-28-1747 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-1750         TCGA-28-1752         TCGA-28-1753 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-1757         TCGA-28-2501         TCGA-28-5208 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-5214         TCGA-32-1970         TCGA-32-1976 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-1978         TCGA-32-1982         TCGA-32-1986 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-1987         TCGA-32-1991         TCGA-32-4210 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-4211         TCGA-32-5222         TCGA-41-2573 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-41-2575         TCGA-41-3392         TCGA-41-3393 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-41-3915         TCGA-41-4097         TCGA-41-5651 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-41-6646         TCGA-74-6573         TCGA-74-6575 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-74-6577         TCGA-74-6578         TCGA-74-6581 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-74-6584         TCGA-76-4926         TCGA-76-4928 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931         TCGA-76-6192 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6193         TCGA-76-6282         TCGA-76-6283 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6285         TCGA-76-6656         TCGA-76-6657 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6660         TCGA-76-6662         TCGA-76-6663 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6664         TCGA-81-5910 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D20V8, multiclass
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                200 
        TCGA-02-0003         TCGA-02-0011         TCGA-02-0068 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-02-0069         TCGA-02-0116         TCGA-02-2470 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-06-0125         TCGA-06-0126 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0128         TCGA-06-0129         TCGA-06-0130 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0154         TCGA-06-0155         TCGA-06-0171 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0189         TCGA-06-0238         TCGA-06-0644 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0650         TCGA-06-0875         TCGA-06-0876 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0877         TCGA-06-0878         TCGA-06-0879 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0882         TCGA-06-0939         TCGA-06-1084 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-1086         TCGA-06-1087         TCGA-06-1800 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-1802         TCGA-06-1804         TCGA-06-1805 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-1806         TCGA-06-2557         TCGA-06-2558 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2562         TCGA-06-2563 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-2564         TCGA-06-2565         TCGA-06-2566 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2570         TCGA-06-5408 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5410         TCGA-06-5411         TCGA-06-5412 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5413         TCGA-06-5414         TCGA-06-5415 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5416         TCGA-06-5418         TCGA-06-5856 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5858         TCGA-06-5859         TCGA-06-6388 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-6389         TCGA-06-6390         TCGA-06-6391 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-6693         TCGA-06-6694         TCGA-06-6695 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-6697         TCGA-06-6698         TCGA-06-6699 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-6700         TCGA-06-6701         TCGA-08-0245 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0344         TCGA-08-0345         TCGA-08-0346 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0347         TCGA-08-0348         TCGA-08-0349 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0350         TCGA-08-0351         TCGA-08-0352 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0353         TCGA-08-0354         TCGA-08-0355 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0356         TCGA-08-0357         TCGA-08-0358 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0359         TCGA-08-0375         TCGA-08-0380 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0386         TCGA-08-0389         TCGA-08-0390 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0392         TCGA-12-0691         TCGA-12-0692 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-1598         TCGA-12-1599         TCGA-12-3646 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-3649         TCGA-12-3650         TCGA-12-3651 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-5301         TCGA-14-0813         TCGA-14-0862 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-14-0871         TCGA-14-1823         TCGA-15-1446 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-15-1447         TCGA-15-1449         TCGA-16-0846 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-16-1460         TCGA-19-0957         TCGA-19-0962 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-1386         TCGA-19-1389         TCGA-19-1390 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-1392         TCGA-19-1786         TCGA-19-1789 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-1791         TCGA-19-2619         TCGA-19-2620 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-2625         TCGA-19-2631         TCGA-19-5947 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-5950         TCGA-19-5951         TCGA-19-5952 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-5953         TCGA-19-5954         TCGA-19-5955 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-5956         TCGA-19-5958         TCGA-19-5959 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1440         TCGA-26-1442 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-26-6173         TCGA-26-6174         TCGA-27-1830 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1833 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1836         TCGA-27-2518 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-2528         TCGA-28-1746         TCGA-28-1747 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-1750         TCGA-28-1752         TCGA-28-1753 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-1757         TCGA-28-2501         TCGA-28-5208 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-5214         TCGA-32-1970         TCGA-32-1976 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-1978         TCGA-32-1982         TCGA-32-1986 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-1987         TCGA-32-1991         TCGA-32-4210 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-4211         TCGA-32-5222         TCGA-41-2573 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-41-2575         TCGA-41-3392         TCGA-41-3393 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-41-3915         TCGA-41-4097         TCGA-41-5651 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-41-6646         TCGA-74-6573         TCGA-74-6575 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-74-6577         TCGA-74-6578         TCGA-74-6581 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-74-6584         TCGA-76-4926         TCGA-76-4928 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931         TCGA-76-6192 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6193         TCGA-76-6282         TCGA-76-6283 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6285         TCGA-76-6656         TCGA-76-6657 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6660         TCGA-76-6662         TCGA-76-6663 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-6664         TCGA-81-5910 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D20V9, multiclass
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2569         TCGA-06-2570 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0386         TCGA-12-0616         TCGA-12-0618 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-0619         TCGA-12-0821         TCGA-12-3650 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-5299         TCGA-14-0781         TCGA-14-0787 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-14-0789         TCGA-14-0790         TCGA-14-0817 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-14-1034         TCGA-14-1823         TCGA-14-1825 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-14-1829         TCGA-14-2554         TCGA-15-0742 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-15-1444         TCGA-16-0846         TCGA-16-1045 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-1390         TCGA-19-1787         TCGA-19-2619 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-2620         TCGA-19-2624         TCGA-19-2625 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-2629         TCGA-19-5960         TCGA-26-1442 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-26-5135         TCGA-26-5136         TCGA-26-5139 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-1830         TCGA-27-1831         TCGA-27-1832 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1835         TCGA-27-1837 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-2519         TCGA-27-2521         TCGA-27-2523 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-2524         TCGA-27-2528         TCGA-28-1747 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-1753         TCGA-28-2509         TCGA-28-2510 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-2513         TCGA-28-2514         TCGA-28-5204 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-5213         TCGA-28-5215         TCGA-28-5216 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-5218         TCGA-28-5220         TCGA-32-1970 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-4931 
"11P GAIN WILD-TYPE" 
D20V10, multiclass
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2569         TCGA-06-2570 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-08-0386         TCGA-12-0616         TCGA-12-0618 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-0619         TCGA-12-0821         TCGA-12-3650 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-12-5299         TCGA-14-0781         TCGA-14-0787 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-14-0789         TCGA-14-0790         TCGA-14-0817 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-14-1034         TCGA-14-1823         TCGA-14-1825 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-14-1829         TCGA-14-2554         TCGA-15-0742 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-15-1444         TCGA-16-0846         TCGA-16-1045 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-1390         TCGA-19-1787         TCGA-19-2619 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-2620         TCGA-19-2624         TCGA-19-2625 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-19-2629         TCGA-19-5960         TCGA-26-1442 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-26-5135         TCGA-26-5136         TCGA-26-5139 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-1830         TCGA-27-1831         TCGA-27-1832 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1835         TCGA-27-1837 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-2519         TCGA-27-2521         TCGA-27-2523 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-27-2524         TCGA-27-2528         TCGA-28-1747 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-1753         TCGA-28-2509         TCGA-28-2510 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-2513         TCGA-28-2514         TCGA-28-5204 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-5213         TCGA-28-5215         TCGA-28-5216 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-28-5218         TCGA-28-5220         TCGA-32-1970 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-76-4931 
"11P GAIN WILD-TYPE" 

Clustering(21) Variable = 11q gain mutation analysis
D21V1, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                2                170
  CLUS_2                4                166
  CLUS_3                0                167
D21V2, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                2                215
  CLUS_2                0                126
  CLUS_3                4                162
D21V3, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                139
  CLUS_2                3                154
  CLUS_3                0                 72
  CLUS_4                2                102
D21V4, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                2                161
  CLUS_2                0                179
  CLUS_3                3                127
D21V5, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                160
  CLUS_2                1                213
  CLUS_3                5                183
D21V6, multiclass
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                108 
        TCGA-06-0650         TCGA-06-1804         TCGA-06-1806 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5299         TCGA-12-5301 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-14-0740         TCGA-14-0781         TCGA-14-0862 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-14-1043         TCGA-14-1395         TCGA-14-1450 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-15-1444         TCGA-19-5947         TCGA-19-5950 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-19-5951         TCGA-19-5952         TCGA-19-5953 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-19-5954         TCGA-19-5955         TCGA-19-5956 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-19-5958         TCGA-19-5959         TCGA-19-5960 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-26-1442         TCGA-26-5132         TCGA-26-5133 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-26-5134         TCGA-26-5135         TCGA-26-5136 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-26-5139         TCGA-26-6173         TCGA-26-6174 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-2501         TCGA-28-2510         TCGA-28-5204 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-5211         TCGA-28-5213         TCGA-28-5214 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-5215         TCGA-28-5216         TCGA-28-5218 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-5219         TCGA-28-5220         TCGA-28-6450 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-32-1979         TCGA-32-1980         TCGA-32-5222 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-41-5651         TCGA-41-6646         TCGA-74-6573 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-74-6575         TCGA-74-6577         TCGA-74-6578 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-74-6581         TCGA-74-6584         TCGA-76-4925 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-76-4931         TCGA-76-4934         TCGA-76-4935 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-76-6191         TCGA-76-6192         TCGA-76-6193 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-76-6280         TCGA-76-6282         TCGA-76-6283 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-76-6285         TCGA-76-6286         TCGA-76-6656 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-76-6657         TCGA-76-6660         TCGA-76-6661 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-76-6662         TCGA-76-6663         TCGA-76-6664 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-81-5910         TCGA-81-5911         TCGA-87-5896 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D21V7, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                 53
  CLUS_2                1                 57
  CLUS_3                0                 44
  CLUS_4                1                 44
D21V8, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                 64
  CLUS_2                0                 33
  CLUS_3                3                101
D21V9, multiclass
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                146 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2569         TCGA-06-2570 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-08-0386         TCGA-12-0616         TCGA-12-0618 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-12-0619         TCGA-12-0821         TCGA-12-3650 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-12-5299         TCGA-14-0781         TCGA-14-0787 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-14-0789         TCGA-14-0790         TCGA-14-0817 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-14-1034         TCGA-14-1823         TCGA-14-1825 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-14-1829         TCGA-14-2554         TCGA-15-0742 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-15-1444         TCGA-16-0846         TCGA-16-1045 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-19-1390         TCGA-19-1787         TCGA-19-2619 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-19-2620         TCGA-19-2624         TCGA-19-2625 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-19-2629         TCGA-19-5960         TCGA-26-1442 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-26-5135         TCGA-26-5136         TCGA-26-5139 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-27-1830         TCGA-27-1831         TCGA-27-1832 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1835         TCGA-27-1837 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-27-2519         TCGA-27-2521         TCGA-27-2523 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-27-2524         TCGA-27-2526         TCGA-27-2528 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-1747         TCGA-28-1753         TCGA-28-2509 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-2510         TCGA-28-2513         TCGA-28-2514 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5213         TCGA-28-5215 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-5216         TCGA-28-5218         TCGA-28-5220 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-32-1970         TCGA-32-1980         TCGA-32-1982 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-32-2615         TCGA-32-2616         TCGA-32-2632 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-32-2634         TCGA-32-2638         TCGA-32-4213 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-32-5222         TCGA-41-2571         TCGA-41-2572 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-41-3915         TCGA-41-4097         TCGA-41-5651 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-76-4925         TCGA-76-4926         TCGA-76-4928 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D21V10, multiclass
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                146 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2569         TCGA-06-2570 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-08-0386         TCGA-12-0616         TCGA-12-0618 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-12-0619         TCGA-12-0821         TCGA-12-3650 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-12-5299         TCGA-14-0781         TCGA-14-0787 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-14-0789         TCGA-14-0790         TCGA-14-0817 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-14-1034         TCGA-14-1823         TCGA-14-1825 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-14-1829         TCGA-14-2554         TCGA-15-0742 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-15-1444         TCGA-16-0846         TCGA-16-1045 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-19-1390         TCGA-19-1787         TCGA-19-2619 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-19-2620         TCGA-19-2624         TCGA-19-2625 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-19-2629         TCGA-19-5960         TCGA-26-1442 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-26-5135         TCGA-26-5136         TCGA-26-5139 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-27-1830         TCGA-27-1831         TCGA-27-1832 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1835         TCGA-27-1837 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-27-2519         TCGA-27-2521         TCGA-27-2523 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-27-2524         TCGA-27-2526         TCGA-27-2528 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-1747         TCGA-28-1753         TCGA-28-2509 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-2510         TCGA-28-2513         TCGA-28-2514 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5213         TCGA-28-5215 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-28-5216         TCGA-28-5218         TCGA-28-5220 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-32-1970         TCGA-32-1980         TCGA-32-1982 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-32-2615         TCGA-32-2616         TCGA-32-2632 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-32-2634         TCGA-32-2638         TCGA-32-4213 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-32-5222         TCGA-41-2571         TCGA-41-2572 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-41-3915         TCGA-41-4097         TCGA-41-5651 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-76-4925         TCGA-76-4926         TCGA-76-4928 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 

Clustering(22) Variable = 12p gain mutation analysis
D22V1, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               15                157
  CLUS_2                9                161
  CLUS_3               14                153
D22V2, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               21                196
  CLUS_2                9                117
  CLUS_3                8                158
D22V3, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               12                127
  CLUS_2               13                144
  CLUS_3                6                 66
  CLUS_4                8                 96
D22V4, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               13                150
  CLUS_2               19                160
  CLUS_3                7                123
D22V5, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               23                138
  CLUS_2                9                205
  CLUS_3               11                177
D22V6, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                 37
  CLUS_2                2                 18
  CLUS_3                1                 23
  CLUS_4                3                 24
D22V7, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                 53
  CLUS_2                5                 53
  CLUS_3                3                 41
  CLUS_4                4                 41
D22V8, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                4                 60
  CLUS_2                1                 32
  CLUS_3                8                 96
D22V9, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                0                 44
  CLUS_2                8                 59
  CLUS_3                2                 34
D22V10, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                7                 59
  CLUS_2                1                 20
  CLUS_3                2                 58

Clustering(23) Variable = 12q gain mutation analysis
D23V1, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               12                160
  CLUS_2                6                164
  CLUS_3               11                156
D23V2, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               16                201
  CLUS_2                9                117
  CLUS_3                4                162
D23V3, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                9                130
  CLUS_2               11                146
  CLUS_3                4                 68
  CLUS_4                7                 97
D23V4, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               10                153
  CLUS_2               16                163
  CLUS_3                5                125
D23V5, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               18                143
  CLUS_2                9                205
  CLUS_3                6                182
D23V6, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                 37
  CLUS_2                2                 18
  CLUS_3                1                 23
  CLUS_4                1                 26
D23V7, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                 53
  CLUS_2                4                 54
  CLUS_3                3                 41
  CLUS_4                3                 42
D23V8, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                5                 59
  CLUS_2                1                 32
  CLUS_3                5                 99
D23V9, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                0                 44
  CLUS_2                6                 61
  CLUS_3                2                 34
D23V10, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                5                 61
  CLUS_2                1                 20
  CLUS_3                2                 58

Clustering(24) Variable = 13q gain mutation analysis
D24V1, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                2                170
  CLUS_2                1                169
  CLUS_3                0                167
D24V2, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                2                215
  CLUS_2                0                126
  CLUS_3                1                165
D24V3, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                0                139
  CLUS_2                3                154
  CLUS_3                0                 72
  CLUS_4                0                104
D24V4, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                0                163
  CLUS_2                2                177
  CLUS_3                1                129
D24V5, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                2                159
  CLUS_2                1                213
  CLUS_3                0                188
D24V6, multiclass
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                108 
        TCGA-06-0650         TCGA-06-1804         TCGA-06-1806 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5299         TCGA-12-5301 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-14-0740         TCGA-14-0781         TCGA-14-0862 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-14-1043         TCGA-14-1395         TCGA-14-1450 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-15-1444         TCGA-19-4065         TCGA-19-5947 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-5950         TCGA-19-5951         TCGA-19-5952 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-5953         TCGA-19-5954         TCGA-19-5955 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-5956         TCGA-19-5958         TCGA-19-5959 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-26-5139         TCGA-26-6173         TCGA-26-6174 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-28-2501         TCGA-28-2510         TCGA-28-5204 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-28-5211         TCGA-28-5213         TCGA-28-5214 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-28-5215         TCGA-28-5216         TCGA-28-5218 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-28-5219         TCGA-28-5220         TCGA-28-6450 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-32-1979         TCGA-32-1980         TCGA-32-5222 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-41-5651         TCGA-41-6646         TCGA-74-6573 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-74-6575         TCGA-74-6577         TCGA-74-6578 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-74-6581         TCGA-74-6584         TCGA-76-4925 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-4931         TCGA-76-4934         TCGA-76-4935 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6191         TCGA-76-6192         TCGA-76-6193 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6280         TCGA-76-6282         TCGA-76-6283 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6285         TCGA-76-6286         TCGA-76-6656 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6657         TCGA-76-6660         TCGA-76-6661 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6662         TCGA-76-6663         TCGA-76-6664 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-81-5910         TCGA-81-5911         TCGA-87-5896 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D24V7, multiclass
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                200 
        TCGA-02-0003         TCGA-02-0011         TCGA-02-0014 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-02-0068         TCGA-02-0069         TCGA-02-0116 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-02-2470         TCGA-02-2485         TCGA-06-0125 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-0126         TCGA-06-0128         TCGA-06-0129 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-0130         TCGA-06-0154         TCGA-06-0155 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-0171         TCGA-06-0189         TCGA-06-0238 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-0644         TCGA-06-0650         TCGA-06-0875 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-0876         TCGA-06-0877         TCGA-06-0878 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-0879         TCGA-06-0882         TCGA-06-0939 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-1084         TCGA-06-1086         TCGA-06-1087 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-1800         TCGA-06-1802         TCGA-06-1804 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-1805         TCGA-06-1806         TCGA-06-2557 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-2558         TCGA-06-2559         TCGA-06-2562 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-2566         TCGA-06-2567         TCGA-06-2570 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0245         TCGA-08-0344         TCGA-08-0345 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0346         TCGA-08-0347         TCGA-08-0348 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0349         TCGA-08-0350         TCGA-08-0351 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0352         TCGA-08-0353         TCGA-08-0354 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0355         TCGA-08-0356         TCGA-08-0357 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0358         TCGA-08-0359         TCGA-08-0375 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0380         TCGA-08-0386         TCGA-08-0389 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0390         TCGA-08-0392         TCGA-12-0691 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-12-0692         TCGA-12-1598         TCGA-12-1599 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-12-3646         TCGA-12-3649         TCGA-12-3650 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-12-3651         TCGA-12-3652         TCGA-12-3653 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5301         TCGA-14-0813 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-14-0862         TCGA-14-0871         TCGA-14-1823 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-15-1446         TCGA-15-1447         TCGA-15-1449 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-16-0846         TCGA-16-1460         TCGA-19-0957 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-0962         TCGA-19-1386         TCGA-19-1389 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-1392         TCGA-19-1786         TCGA-19-1789 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-1791         TCGA-19-2619         TCGA-19-2620 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-2625         TCGA-19-2631         TCGA-19-5947 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-5950         TCGA-19-5951         TCGA-19-5952 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-5953         TCGA-19-5954         TCGA-19-5955 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-5956         TCGA-19-5958         TCGA-19-5959 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1440         TCGA-26-1442 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-26-6173         TCGA-26-6174         TCGA-27-1830 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1833 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1836         TCGA-27-2518 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-27-2528         TCGA-28-1746         TCGA-28-1747 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-28-1750         TCGA-28-1752         TCGA-28-1753 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-28-1757         TCGA-28-2501         TCGA-28-5208 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-28-5214         TCGA-32-1970         TCGA-32-1976 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-32-1978         TCGA-32-1982         TCGA-32-1986 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-32-1987         TCGA-32-1991         TCGA-32-4210 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-32-4211         TCGA-32-5222         TCGA-41-2573 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-41-2575         TCGA-41-3392         TCGA-41-3393 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-41-3915         TCGA-41-4097         TCGA-41-5651 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-41-6646         TCGA-74-6573         TCGA-74-6575 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-74-6577         TCGA-74-6578         TCGA-74-6581 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-74-6584         TCGA-76-4926         TCGA-76-4928 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931         TCGA-76-6192 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6193         TCGA-76-6282         TCGA-76-6283 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6285         TCGA-76-6656         TCGA-76-6657 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6660         TCGA-76-6662         TCGA-76-6663 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6664         TCGA-81-5910 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D24V8, multiclass
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                200 
        TCGA-02-0003         TCGA-02-0011         TCGA-02-0014 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-02-0068         TCGA-02-0069         TCGA-02-0116 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-02-2470         TCGA-02-2485         TCGA-06-0125 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-0126         TCGA-06-0128         TCGA-06-0129 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-0130         TCGA-06-0154         TCGA-06-0155 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-0171         TCGA-06-0189         TCGA-06-0238 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-0644         TCGA-06-0650         TCGA-06-0875 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-0876         TCGA-06-0877         TCGA-06-0878 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-0879         TCGA-06-0882         TCGA-06-0939 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-1084         TCGA-06-1086         TCGA-06-1087 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-1800         TCGA-06-1802         TCGA-06-1804 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-1805         TCGA-06-1806         TCGA-06-2557 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-2558         TCGA-06-2559         TCGA-06-2562 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-2566         TCGA-06-2567         TCGA-06-2570 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0245         TCGA-08-0344         TCGA-08-0345 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0346         TCGA-08-0347         TCGA-08-0348 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0349         TCGA-08-0350         TCGA-08-0351 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0352         TCGA-08-0353         TCGA-08-0354 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0355         TCGA-08-0356         TCGA-08-0357 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0358         TCGA-08-0359         TCGA-08-0375 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0380         TCGA-08-0386         TCGA-08-0389 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-08-0390         TCGA-08-0392         TCGA-12-0691 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-12-0692         TCGA-12-1598         TCGA-12-1599 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-12-3646         TCGA-12-3649         TCGA-12-3650 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-12-3651         TCGA-12-3652         TCGA-12-3653 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5301         TCGA-14-0813 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-14-0862         TCGA-14-0871         TCGA-14-1823 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-15-1446         TCGA-15-1447         TCGA-15-1449 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-16-0846         TCGA-16-1460         TCGA-19-0957 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-0962         TCGA-19-1386         TCGA-19-1389 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-1392         TCGA-19-1786         TCGA-19-1789 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-1791         TCGA-19-2619         TCGA-19-2620 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-2625         TCGA-19-2631         TCGA-19-5947 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-5950         TCGA-19-5951         TCGA-19-5952 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-5953         TCGA-19-5954         TCGA-19-5955 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-5956         TCGA-19-5958         TCGA-19-5959 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1440         TCGA-26-1442 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-26-6173         TCGA-26-6174         TCGA-27-1830 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1833 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1836         TCGA-27-2518 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-27-2528         TCGA-28-1746         TCGA-28-1747 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-28-1750         TCGA-28-1752         TCGA-28-1753 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-28-1757         TCGA-28-2501         TCGA-28-5208 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-28-5214         TCGA-32-1970         TCGA-32-1976 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-32-1978         TCGA-32-1982         TCGA-32-1986 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-32-1987         TCGA-32-1991         TCGA-32-4210 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-32-4211         TCGA-32-5222         TCGA-41-2573 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-41-2575         TCGA-41-3392         TCGA-41-3393 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-41-3915         TCGA-41-4097         TCGA-41-5651 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-41-6646         TCGA-74-6573         TCGA-74-6575 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-74-6577         TCGA-74-6578         TCGA-74-6581 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-74-6584         TCGA-76-4926         TCGA-76-4928 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931         TCGA-76-6192 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6193         TCGA-76-6282         TCGA-76-6283 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6285         TCGA-76-6656         TCGA-76-6657 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6660         TCGA-76-6662         TCGA-76-6663 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-76-6664         TCGA-81-5910 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D24V9, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                1                 43
  CLUS_2                1                 66
  CLUS_3                1                 35
D24V10, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                1                 65
  CLUS_2                1                 20
  CLUS_3                1                 59

Clustering(25) Variable = 14q gain mutation analysis
D25V1, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                3                169
  CLUS_2                1                169
  CLUS_3                2                165
D25V2, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                3                214
  CLUS_2                2                124
  CLUS_3                1                165
D25V3, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                5                134
  CLUS_2                0                157
  CLUS_3                1                 71
  CLUS_4                1                103
D25V4, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                4                159
  CLUS_2                2                177
  CLUS_3                1                129
D25V5, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                160
  CLUS_2                4                210
  CLUS_3                2                186
D25V6, multiclass
D25V7, multiclass
D25V8, multiclass
D25V9, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2570         TCGA-06-5408 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-5410         TCGA-06-5411         TCGA-06-5412 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-5413         TCGA-06-5414         TCGA-06-5415 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-5416         TCGA-06-5418         TCGA-06-5856 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-5858         TCGA-06-5859         TCGA-08-0386 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-12-0616         TCGA-12-0618         TCGA-12-0619 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-12-0821         TCGA-12-3650         TCGA-12-3652 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-12-3653         TCGA-12-5295         TCGA-12-5299 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-14-0781         TCGA-14-0787         TCGA-14-0789 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-14-0790         TCGA-14-0817         TCGA-14-1034 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-14-1823         TCGA-14-1825         TCGA-14-1829 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-14-2554         TCGA-15-0742         TCGA-15-1444 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-16-0846         TCGA-16-1045         TCGA-19-1390 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2620 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-19-2624         TCGA-19-2625         TCGA-19-2629 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-19-4065         TCGA-19-5960         TCGA-26-1442 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-26-5135         TCGA-26-5136         TCGA-26-5139 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-27-1830         TCGA-27-1831         TCGA-27-1832 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1835         TCGA-27-1837 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-27-2519         TCGA-27-2521         TCGA-27-2523 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-27-2524         TCGA-27-2526         TCGA-27-2528 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-28-1747         TCGA-28-1753         TCGA-28-2509 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-28-2510         TCGA-28-2513         TCGA-28-2514 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5213         TCGA-28-5215 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-28-5216         TCGA-28-5218         TCGA-28-5220 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-32-1970         TCGA-32-1980         TCGA-32-1982 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-32-2615         TCGA-32-2616         TCGA-32-2634 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-76-4931 
"14Q GAIN WILD-TYPE" 
D25V10, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2570         TCGA-06-5408 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-5410         TCGA-06-5411         TCGA-06-5412 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-5413         TCGA-06-5414         TCGA-06-5415 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-5416         TCGA-06-5418         TCGA-06-5856 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-06-5858         TCGA-06-5859         TCGA-08-0386 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-12-0616         TCGA-12-0618         TCGA-12-0619 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-12-0821         TCGA-12-3650         TCGA-12-3652 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-12-3653         TCGA-12-5295         TCGA-12-5299 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-14-0781         TCGA-14-0787         TCGA-14-0789 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-14-0790         TCGA-14-0817         TCGA-14-1034 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-14-1823         TCGA-14-1825         TCGA-14-1829 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-14-2554         TCGA-15-0742         TCGA-15-1444 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-16-0846         TCGA-16-1045         TCGA-19-1390 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2620 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-19-2624         TCGA-19-2625         TCGA-19-2629 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-19-4065         TCGA-19-5960         TCGA-26-1442 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-26-5135         TCGA-26-5136         TCGA-26-5139 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-27-1830         TCGA-27-1831         TCGA-27-1832 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1835         TCGA-27-1837 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-27-2519         TCGA-27-2521         TCGA-27-2523 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-27-2524         TCGA-27-2526         TCGA-27-2528 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-28-1747         TCGA-28-1753         TCGA-28-2509 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-28-2510         TCGA-28-2513         TCGA-28-2514 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5213         TCGA-28-5215 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-28-5216         TCGA-28-5218         TCGA-28-5220 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-32-1970         TCGA-32-1980         TCGA-32-1982 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-32-2615         TCGA-32-2616         TCGA-32-2634 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-76-4931 
"14Q GAIN WILD-TYPE" 

Clustering(26) Variable = 15q gain mutation analysis
D26V1, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                3                169
  CLUS_2                2                168
  CLUS_3                0                167
D26V2, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                3                214
  CLUS_2                0                126
  CLUS_3                2                164
D26V3, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                3                136
  CLUS_2                1                156
  CLUS_3                0                 72
  CLUS_4                2                102
D26V4, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                3                160
  CLUS_2                1                178
  CLUS_3                2                128
D26V5, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                5                156
  CLUS_2                1                213
  CLUS_3                0                188
D26V6, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                108 
        TCGA-06-0650         TCGA-06-1804         TCGA-06-1806 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5299         TCGA-12-5301 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-14-0740         TCGA-14-0781         TCGA-14-0862 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-14-1043         TCGA-14-1395         TCGA-14-1450 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-15-1444         TCGA-19-4065         TCGA-19-5947 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-5950         TCGA-19-5951         TCGA-19-5952 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-5953         TCGA-19-5954         TCGA-19-5955 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-5956         TCGA-19-5958         TCGA-19-5959 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-26-5136         TCGA-26-5139         TCGA-26-6173 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-26-6174         TCGA-28-2501         TCGA-28-2510 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5211         TCGA-28-5213 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-5214         TCGA-28-5215         TCGA-28-5216 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-5219         TCGA-28-5220         TCGA-28-6450 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-1979         TCGA-32-1980         TCGA-32-5222 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-41-5651         TCGA-41-6646         TCGA-74-6573 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-74-6575         TCGA-74-6577         TCGA-74-6578 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-74-6581         TCGA-74-6584         TCGA-76-4925 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-4931         TCGA-76-4934         TCGA-76-4935 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6191         TCGA-76-6192         TCGA-76-6193 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6280         TCGA-76-6282         TCGA-76-6283 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6285         TCGA-76-6286         TCGA-76-6656 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6657         TCGA-76-6660         TCGA-76-6661 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6662         TCGA-76-6663         TCGA-76-6664 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-81-5910         TCGA-81-5911         TCGA-87-5896 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
D26V7, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                200 
        TCGA-02-0003         TCGA-02-0011         TCGA-02-0014 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-02-0068         TCGA-02-0069         TCGA-02-0116 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-02-2470         TCGA-02-2485         TCGA-06-0125 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0126         TCGA-06-0128         TCGA-06-0129 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0130         TCGA-06-0154         TCGA-06-0155 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0171         TCGA-06-0189         TCGA-06-0238 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0644         TCGA-06-0650         TCGA-06-0875 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0876         TCGA-06-0877         TCGA-06-0878 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0879         TCGA-06-0882         TCGA-06-0939 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-1084         TCGA-06-1086         TCGA-06-1087 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-1800         TCGA-06-1802         TCGA-06-1804 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-1805         TCGA-06-1806         TCGA-06-2557 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-2558         TCGA-06-2559         TCGA-06-2562 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-2566         TCGA-06-2567         TCGA-06-2570 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0245         TCGA-08-0344         TCGA-08-0345 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0346         TCGA-08-0347         TCGA-08-0348 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0349         TCGA-08-0350         TCGA-08-0351 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0352         TCGA-08-0353         TCGA-08-0354 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0355         TCGA-08-0356         TCGA-08-0357 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0358         TCGA-08-0359         TCGA-08-0375 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0380         TCGA-08-0386         TCGA-08-0389 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0390         TCGA-08-0392         TCGA-12-0691 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-0692         TCGA-12-1598         TCGA-12-1599 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-3646         TCGA-12-3649         TCGA-12-3650 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-3651         TCGA-12-3652         TCGA-12-3653 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5301         TCGA-14-0813 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-14-0862         TCGA-14-0871         TCGA-15-1446 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-15-1447         TCGA-15-1449         TCGA-16-0846 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-16-1460         TCGA-19-0957         TCGA-19-0962 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-1386         TCGA-19-1389         TCGA-19-1390 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-1392         TCGA-19-1786         TCGA-19-1789 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-1791         TCGA-19-2619         TCGA-19-2620 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-2625         TCGA-19-2631         TCGA-19-5947 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-5950         TCGA-19-5951         TCGA-19-5952 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-5953         TCGA-19-5954         TCGA-19-5955 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-5956         TCGA-19-5958         TCGA-19-5959 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1440         TCGA-26-1442 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-26-6173         TCGA-26-6174         TCGA-27-1830 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1833 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1836         TCGA-27-2518 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-2528         TCGA-28-1746         TCGA-28-1747 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-1750         TCGA-28-1752         TCGA-28-1753 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-1757         TCGA-28-2501         TCGA-28-5208 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-5214         TCGA-32-1970         TCGA-32-1976 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-1978         TCGA-32-1982         TCGA-32-1986 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-1987         TCGA-32-1991         TCGA-32-4210 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-4211         TCGA-32-5222         TCGA-41-2573 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-41-2575         TCGA-41-3392         TCGA-41-3393 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-41-3915         TCGA-41-4097         TCGA-41-5651 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-41-6646         TCGA-74-6573         TCGA-74-6575 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-74-6577         TCGA-74-6578         TCGA-74-6581 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-74-6584         TCGA-76-4926         TCGA-76-4928 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931         TCGA-76-6192 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6193         TCGA-76-6282         TCGA-76-6283 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6285         TCGA-76-6656         TCGA-76-6657 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6660         TCGA-76-6662         TCGA-76-6663 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6664         TCGA-81-5910 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
D26V8, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                200 
        TCGA-02-0003         TCGA-02-0011         TCGA-02-0014 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-02-0068         TCGA-02-0069         TCGA-02-0116 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-02-2470         TCGA-02-2485         TCGA-06-0125 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0126         TCGA-06-0128         TCGA-06-0129 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0130         TCGA-06-0154         TCGA-06-0155 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0171         TCGA-06-0189         TCGA-06-0238 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0644         TCGA-06-0650         TCGA-06-0875 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0876         TCGA-06-0877         TCGA-06-0878 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0879         TCGA-06-0882         TCGA-06-0939 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-1084         TCGA-06-1086         TCGA-06-1087 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-1800         TCGA-06-1802         TCGA-06-1804 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-1805         TCGA-06-1806         TCGA-06-2557 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-2558         TCGA-06-2559         TCGA-06-2562 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-2566         TCGA-06-2567         TCGA-06-2570 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0245         TCGA-08-0344         TCGA-08-0345 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0346         TCGA-08-0347         TCGA-08-0348 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0349         TCGA-08-0350         TCGA-08-0351 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0352         TCGA-08-0353         TCGA-08-0354 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0355         TCGA-08-0356         TCGA-08-0357 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0358         TCGA-08-0359         TCGA-08-0375 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0380         TCGA-08-0386         TCGA-08-0389 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0390         TCGA-08-0392         TCGA-12-0691 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-0692         TCGA-12-1598         TCGA-12-1599 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-3646         TCGA-12-3649         TCGA-12-3650 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-3651         TCGA-12-3652         TCGA-12-3653 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5301         TCGA-14-0813 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-14-0862         TCGA-14-0871         TCGA-15-1446 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-15-1447         TCGA-15-1449         TCGA-16-0846 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-16-1460         TCGA-19-0957         TCGA-19-0962 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-1386         TCGA-19-1389         TCGA-19-1390 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-1392         TCGA-19-1786         TCGA-19-1789 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-1791         TCGA-19-2619         TCGA-19-2620 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-2625         TCGA-19-2631         TCGA-19-5947 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-5950         TCGA-19-5951         TCGA-19-5952 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-5953         TCGA-19-5954         TCGA-19-5955 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-5956         TCGA-19-5958         TCGA-19-5959 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1440         TCGA-26-1442 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-26-6173         TCGA-26-6174         TCGA-27-1830 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1833 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1836         TCGA-27-2518 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-2528         TCGA-28-1746         TCGA-28-1747 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-1750         TCGA-28-1752         TCGA-28-1753 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-1757         TCGA-28-2501         TCGA-28-5208 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-5214         TCGA-32-1970         TCGA-32-1976 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-1978         TCGA-32-1982         TCGA-32-1986 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-1987         TCGA-32-1991         TCGA-32-4210 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-4211         TCGA-32-5222         TCGA-41-2573 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-41-2575         TCGA-41-3392         TCGA-41-3393 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-41-3915         TCGA-41-4097         TCGA-41-5651 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-41-6646         TCGA-74-6573         TCGA-74-6575 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-74-6577         TCGA-74-6578         TCGA-74-6581 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-74-6584         TCGA-76-4926         TCGA-76-4928 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931         TCGA-76-6192 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6193         TCGA-76-6282         TCGA-76-6283 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6285         TCGA-76-6656         TCGA-76-6657 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6660         TCGA-76-6662         TCGA-76-6663 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-6664         TCGA-81-5910 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
D26V9, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2569         TCGA-06-2570 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0386         TCGA-12-0616         TCGA-12-0618 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-0619         TCGA-12-0821         TCGA-12-3650 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-5299         TCGA-14-0781         TCGA-14-0787 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-14-0789         TCGA-14-0790         TCGA-14-0817 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-14-1034         TCGA-14-1825         TCGA-14-1829 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-14-2554         TCGA-15-0742         TCGA-15-1444 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-16-0846         TCGA-16-1045         TCGA-19-1390 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2620 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-2624         TCGA-19-2625         TCGA-19-2629 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-4065         TCGA-19-5960         TCGA-26-1442 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-26-5135         TCGA-26-5136         TCGA-26-5139 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-1830         TCGA-27-1831         TCGA-27-1832 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1835         TCGA-27-1837 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-2519         TCGA-27-2521         TCGA-27-2523 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-2524         TCGA-27-2526         TCGA-27-2528 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-1747         TCGA-28-1753         TCGA-28-2509 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-2510         TCGA-28-2513         TCGA-28-2514 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5213         TCGA-28-5215 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-5216         TCGA-28-5220         TCGA-32-1970 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-4931 
"15Q GAIN WILD-TYPE" 
D26V10, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2569         TCGA-06-2570 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-08-0386         TCGA-12-0616         TCGA-12-0618 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-0619         TCGA-12-0821         TCGA-12-3650 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-12-5299         TCGA-14-0781         TCGA-14-0787 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-14-0789         TCGA-14-0790         TCGA-14-0817 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-14-1034         TCGA-14-1825         TCGA-14-1829 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-14-2554         TCGA-15-0742         TCGA-15-1444 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-16-0846         TCGA-16-1045         TCGA-19-1390 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2620 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-2624         TCGA-19-2625         TCGA-19-2629 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-19-4065         TCGA-19-5960         TCGA-26-1442 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-26-5135         TCGA-26-5136         TCGA-26-5139 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-1830         TCGA-27-1831         TCGA-27-1832 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1835         TCGA-27-1837 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-2519         TCGA-27-2521         TCGA-27-2523 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-27-2524         TCGA-27-2526         TCGA-27-2528 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-1747         TCGA-28-1753         TCGA-28-2509 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-2510         TCGA-28-2513         TCGA-28-2514 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5213         TCGA-28-5215 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-28-5216         TCGA-28-5220         TCGA-32-1970 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-76-4931 
"15Q GAIN WILD-TYPE" 

Clustering(27) Variable = 16p gain mutation analysis
D27V1, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                5                167
  CLUS_2               11                159
  CLUS_3                2                165
D27V2, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                6                211
  CLUS_2                3                123
  CLUS_3                9                157
D27V3, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                3                136
  CLUS_2                8                149
  CLUS_3                3                 69
  CLUS_4                4                100
D27V4, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                4                159
  CLUS_2                6                173
  CLUS_3                8                122
D27V5, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               10                151
  CLUS_2                2                212
  CLUS_3                6                182
D27V6, multiclass
D27V7, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                4                 50
  CLUS_2                2                 56
  CLUS_3                0                 44
  CLUS_4                1                 44
D27V8, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                 63
  CLUS_2                2                 31
  CLUS_3                4                100
D27V9, multiclass
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2559 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-2561         TCGA-06-2562         TCGA-06-2563 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-2564         TCGA-06-2565         TCGA-06-2569 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-2570         TCGA-06-5408         TCGA-06-5410 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-5411         TCGA-06-5412         TCGA-06-5413 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-5414         TCGA-06-5415         TCGA-06-5416 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-5418         TCGA-06-5856         TCGA-06-5858 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-5859         TCGA-08-0386         TCGA-12-0616 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-12-0618         TCGA-12-0619         TCGA-12-0821 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-12-3650         TCGA-12-3652         TCGA-12-3653 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5299         TCGA-14-0781 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-14-0787         TCGA-14-0789         TCGA-14-0790 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-14-0817         TCGA-14-1034         TCGA-14-1823 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-14-1825         TCGA-14-1829         TCGA-14-2554 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-15-0742         TCGA-15-1444         TCGA-16-0846 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-16-1045         TCGA-19-1390         TCGA-19-1787 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-19-2619         TCGA-19-2620         TCGA-19-2624 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-19-2625         TCGA-19-2629         TCGA-19-4065 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-26-5136         TCGA-26-5139         TCGA-27-1830 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1834 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-27-1835         TCGA-27-1837         TCGA-27-2519 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-27-2521         TCGA-27-2523         TCGA-27-2524 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-27-2526         TCGA-27-2528         TCGA-28-1747 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-28-1753         TCGA-28-2509         TCGA-28-2510 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-28-2513         TCGA-28-2514         TCGA-28-5204 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-28-5213         TCGA-28-5215         TCGA-28-5216 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-28-5218         TCGA-28-5220         TCGA-32-1970 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-76-4931 
"16P GAIN WILD-TYPE" 
D27V10, multiclass
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2559 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-2561         TCGA-06-2562         TCGA-06-2563 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-2564         TCGA-06-2565         TCGA-06-2569 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-2570         TCGA-06-5408         TCGA-06-5410 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-5411         TCGA-06-5412         TCGA-06-5413 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-5414         TCGA-06-5415         TCGA-06-5416 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-5418         TCGA-06-5856         TCGA-06-5858 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-06-5859         TCGA-08-0386         TCGA-12-0616 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-12-0618         TCGA-12-0619         TCGA-12-0821 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-12-3650         TCGA-12-3652         TCGA-12-3653 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5299         TCGA-14-0781 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-14-0787         TCGA-14-0789         TCGA-14-0790 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-14-0817         TCGA-14-1034         TCGA-14-1823 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-14-1825         TCGA-14-1829         TCGA-14-2554 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-15-0742         TCGA-15-1444         TCGA-16-0846 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-16-1045         TCGA-19-1390         TCGA-19-1787 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-19-2619         TCGA-19-2620         TCGA-19-2624 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-19-2625         TCGA-19-2629         TCGA-19-4065 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-26-5136         TCGA-26-5139         TCGA-27-1830 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1834 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-27-1835         TCGA-27-1837         TCGA-27-2519 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-27-2521         TCGA-27-2523         TCGA-27-2524 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-27-2526         TCGA-27-2528         TCGA-28-1747 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-28-1753         TCGA-28-2509         TCGA-28-2510 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-28-2513         TCGA-28-2514         TCGA-28-5204 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-28-5213         TCGA-28-5215         TCGA-28-5216 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-28-5218         TCGA-28-5220         TCGA-32-1970 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-76-4931 
"16P GAIN WILD-TYPE" 

Clustering(28) Variable = 16q gain mutation analysis
D28V1, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                4                168
  CLUS_2               11                159
  CLUS_3                3                164
D28V2, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                5                212
  CLUS_2                4                122
  CLUS_3                9                157
D28V3, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                3                136
  CLUS_2                8                149
  CLUS_3                4                 68
  CLUS_4                3                101
D28V4, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                3                160
  CLUS_2                5                174
  CLUS_3               10                120
D28V5, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               10                151
  CLUS_2                2                212
  CLUS_3                6                182
D28V6, multiclass
D28V7, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                3                 51
  CLUS_2                3                 55
  CLUS_3                0                 44
  CLUS_4                1                 44
D28V8, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                 63
  CLUS_2                2                 31
  CLUS_3                4                100
D28V9, multiclass
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2559 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-2561         TCGA-06-2562         TCGA-06-2563 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-2564         TCGA-06-2565         TCGA-06-2567 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-2569         TCGA-06-2570         TCGA-06-5408 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-5410         TCGA-06-5411         TCGA-06-5412 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-5413         TCGA-06-5414         TCGA-06-5415 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-5416         TCGA-06-5418         TCGA-06-5856 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-5858         TCGA-06-5859         TCGA-08-0386 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-12-0616         TCGA-12-0618         TCGA-12-0619 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-12-0821         TCGA-12-3650         TCGA-12-3652 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-12-3653         TCGA-12-5295         TCGA-12-5299 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-14-0781         TCGA-14-0787         TCGA-14-0789 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-14-0790         TCGA-14-0817         TCGA-14-1034 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-14-1823         TCGA-14-1825         TCGA-14-1829 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-14-2554         TCGA-15-0742         TCGA-15-1444 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-16-0846         TCGA-16-1045         TCGA-19-1390 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2624 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-19-2625         TCGA-19-2629         TCGA-19-4065 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-26-5136         TCGA-26-5139         TCGA-27-1830 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1834 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-27-1835         TCGA-27-1837         TCGA-27-2519 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-27-2521         TCGA-27-2523         TCGA-27-2524 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-27-2526         TCGA-27-2528         TCGA-28-1747 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-28-1753         TCGA-28-2509         TCGA-28-2510 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-28-2513         TCGA-28-2514         TCGA-28-5204 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-28-5213         TCGA-28-5215         TCGA-28-5216 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-28-5218         TCGA-28-5220         TCGA-32-1970 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-76-4931 
"16Q GAIN WILD-TYPE" 
D28V10, multiclass
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2559 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-2561         TCGA-06-2562         TCGA-06-2563 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-2564         TCGA-06-2565         TCGA-06-2567 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-2569         TCGA-06-2570         TCGA-06-5408 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-5410         TCGA-06-5411         TCGA-06-5412 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-5413         TCGA-06-5414         TCGA-06-5415 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-5416         TCGA-06-5418         TCGA-06-5856 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-06-5858         TCGA-06-5859         TCGA-08-0386 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-12-0616         TCGA-12-0618         TCGA-12-0619 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-12-0821         TCGA-12-3650         TCGA-12-3652 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-12-3653         TCGA-12-5295         TCGA-12-5299 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-14-0781         TCGA-14-0787         TCGA-14-0789 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-14-0790         TCGA-14-0817         TCGA-14-1034 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-14-1823         TCGA-14-1825         TCGA-14-1829 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-14-2554         TCGA-15-0742         TCGA-15-1444 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-16-0846         TCGA-16-1045         TCGA-19-1390 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2624 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-19-2625         TCGA-19-2629         TCGA-19-4065 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-26-5136         TCGA-26-5139         TCGA-27-1830 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1834 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-27-1835         TCGA-27-1837         TCGA-27-2519 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-27-2521         TCGA-27-2523         TCGA-27-2524 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-27-2526         TCGA-27-2528         TCGA-28-1747 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-28-1753         TCGA-28-2509         TCGA-28-2510 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-28-2513         TCGA-28-2514         TCGA-28-5204 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-28-5213         TCGA-28-5215         TCGA-28-5216 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-28-5218         TCGA-28-5220         TCGA-32-1970 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-76-4931 
"16Q GAIN WILD-TYPE" 

Clustering(29) Variable = 17p gain mutation analysis
D29V1, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                3                169
  CLUS_2                7                163
  CLUS_3                0                167
D29V2, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                4                213
  CLUS_2                1                125
  CLUS_3                5                161
D29V3, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                3                136
  CLUS_2                5                152
  CLUS_3                2                 70
  CLUS_4                1                103
D29V4, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                2                161
  CLUS_2                4                175
  CLUS_3                5                125
D29V5, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                6                155
  CLUS_2                4                210
  CLUS_3                1                187
D29V6, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                107 
        TCGA-06-0650         TCGA-06-1804         TCGA-06-1806 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5299         TCGA-14-0740 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-14-0781         TCGA-14-0862         TCGA-14-1043 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-14-1395         TCGA-14-1450         TCGA-15-1444 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-19-4065         TCGA-19-5947         TCGA-19-5950 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-19-5951         TCGA-19-5952         TCGA-19-5953 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-19-5954         TCGA-19-5955         TCGA-19-5956 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-19-5958         TCGA-19-5959         TCGA-19-5960 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-26-1442         TCGA-26-5132         TCGA-26-5133 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-26-5134         TCGA-26-5135         TCGA-26-5136 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-26-5139         TCGA-26-6173         TCGA-26-6174 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-2501         TCGA-28-2510         TCGA-28-5204 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-5211         TCGA-28-5213         TCGA-28-5214 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-5215         TCGA-28-5216         TCGA-28-5219 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-5220         TCGA-28-6450         TCGA-32-1979 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-5222         TCGA-41-5651 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-41-6646         TCGA-74-6573         TCGA-74-6575 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-74-6577         TCGA-74-6578         TCGA-74-6581 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-74-6584         TCGA-76-4925         TCGA-76-4926 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-76-4928         TCGA-76-4929         TCGA-76-4931 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-76-4934         TCGA-76-4935         TCGA-76-6191 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-76-6192         TCGA-76-6193         TCGA-76-6280 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-76-6282         TCGA-76-6283         TCGA-76-6285 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-76-6286         TCGA-76-6656         TCGA-76-6657 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-76-6660         TCGA-76-6661         TCGA-76-6662 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-76-6663         TCGA-76-6664         TCGA-81-5910 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-81-5911         TCGA-87-5896 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D29V7, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                1                 53
  CLUS_2                1                 57
  CLUS_3                0                 44
  CLUS_4                1                 44
D29V8, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                0                 64
  CLUS_2                1                 32
  CLUS_3                2                102
D29V9, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                146 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2569         TCGA-06-2570 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-08-0386         TCGA-12-0616         TCGA-12-0618 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-12-0619         TCGA-12-0821         TCGA-12-3650 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-12-5299         TCGA-14-0781         TCGA-14-0787 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-14-0789         TCGA-14-0790         TCGA-14-0817 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-14-1034         TCGA-14-1823         TCGA-14-1825 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-14-1829         TCGA-14-2554         TCGA-15-0742 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-15-1444         TCGA-16-0846         TCGA-16-1045 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-19-1390         TCGA-19-1787         TCGA-19-2619 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-19-2620         TCGA-19-2624         TCGA-19-2625 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-19-2629         TCGA-19-4065         TCGA-19-5960 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-26-1442         TCGA-26-5132         TCGA-26-5133 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-26-5134         TCGA-26-5135         TCGA-26-5136 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-26-5139         TCGA-27-1830         TCGA-27-1831 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-27-1832         TCGA-27-1834         TCGA-27-1835 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-27-1837         TCGA-27-2519         TCGA-27-2521 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-27-2523         TCGA-27-2524         TCGA-27-2526 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-27-2528         TCGA-28-1747         TCGA-28-1753 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-2509         TCGA-28-2510         TCGA-28-2513 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-2514         TCGA-28-5204         TCGA-28-5207 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-5208         TCGA-28-5209         TCGA-28-5213 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-5215         TCGA-28-5216         TCGA-28-5220 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-32-1970         TCGA-32-1980         TCGA-32-1982 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-32-2615         TCGA-32-2616         TCGA-32-2632 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-32-2634         TCGA-32-2638         TCGA-32-4213 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-32-5222         TCGA-41-2571         TCGA-41-2572 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-41-3915         TCGA-41-4097         TCGA-41-5651 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-76-4925         TCGA-76-4926         TCGA-76-4928 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D29V10, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                146 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2569         TCGA-06-2570 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-08-0386         TCGA-12-0616         TCGA-12-0618 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-12-0619         TCGA-12-0821         TCGA-12-3650 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-12-5299         TCGA-14-0781         TCGA-14-0787 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-14-0789         TCGA-14-0790         TCGA-14-0817 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-14-1034         TCGA-14-1823         TCGA-14-1825 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-14-1829         TCGA-14-2554         TCGA-15-0742 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-15-1444         TCGA-16-0846         TCGA-16-1045 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-19-1390         TCGA-19-1787         TCGA-19-2619 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-19-2620         TCGA-19-2624         TCGA-19-2625 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-19-2629         TCGA-19-4065         TCGA-19-5960 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-26-1442         TCGA-26-5132         TCGA-26-5133 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-26-5134         TCGA-26-5135         TCGA-26-5136 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-26-5139         TCGA-27-1830         TCGA-27-1831 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-27-1832         TCGA-27-1834         TCGA-27-1835 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-27-1837         TCGA-27-2519         TCGA-27-2521 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-27-2523         TCGA-27-2524         TCGA-27-2526 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-27-2528         TCGA-28-1747         TCGA-28-1753 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-2509         TCGA-28-2510         TCGA-28-2513 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-2514         TCGA-28-5204         TCGA-28-5207 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-5208         TCGA-28-5209         TCGA-28-5213 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-28-5215         TCGA-28-5216         TCGA-28-5220 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-32-1970         TCGA-32-1980         TCGA-32-1982 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-32-2615         TCGA-32-2616         TCGA-32-2632 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-32-2634         TCGA-32-2638         TCGA-32-4213 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-32-5222         TCGA-41-2571         TCGA-41-2572 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-41-3915         TCGA-41-4097         TCGA-41-5651 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-76-4925         TCGA-76-4926         TCGA-76-4928 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 

Clustering(30) Variable = 17q gain mutation analysis
D30V1, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                6                166
  CLUS_2                9                161
  CLUS_3                3                164
D30V2, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                8                209
  CLUS_2                4                122
  CLUS_3                6                160
D30V3, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                4                135
  CLUS_2                8                149
  CLUS_3                3                 69
  CLUS_4                4                100
D30V4, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                5                158
  CLUS_2                7                172
  CLUS_3                7                123
D30V5, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               10                151
  CLUS_2                6                208
  CLUS_3                3                185
D30V6, multiclass
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 2                107 
        TCGA-06-0650         TCGA-06-1804         TCGA-06-1806 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5299         TCGA-14-0740 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-14-0781         TCGA-14-0862         TCGA-14-1043 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-14-1395         TCGA-14-1450         TCGA-15-1444 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-19-4065         TCGA-19-5947         TCGA-19-5950 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-19-5951         TCGA-19-5952         TCGA-19-5953 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-19-5954         TCGA-19-5955         TCGA-19-5956 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-19-5958         TCGA-19-5959         TCGA-19-5960 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-26-1442         TCGA-26-5132         TCGA-26-5133 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-26-5134         TCGA-26-5135         TCGA-26-5136 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-26-5139         TCGA-26-6173         TCGA-26-6174 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-28-2501         TCGA-28-2510         TCGA-28-5204 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-28-5211         TCGA-28-5213         TCGA-28-5214 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-28-5215         TCGA-28-5216         TCGA-28-5219 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-28-5220         TCGA-28-6450         TCGA-32-1979 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-5222         TCGA-41-5651 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-41-6646         TCGA-74-6573         TCGA-74-6575 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-74-6577         TCGA-74-6578         TCGA-74-6581 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-74-6584         TCGA-76-4925         TCGA-76-4926 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-76-4928         TCGA-76-4929         TCGA-76-4931 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-76-4934         TCGA-76-4935         TCGA-76-6191 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-76-6192         TCGA-76-6193         TCGA-76-6280 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-76-6282         TCGA-76-6283         TCGA-76-6285 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-76-6286         TCGA-76-6656         TCGA-76-6657 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-76-6660         TCGA-76-6661         TCGA-76-6662 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-76-6663         TCGA-76-6664         TCGA-81-5910 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-81-5911         TCGA-87-5896 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
D30V7, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                2                 52
  CLUS_2                1                 57
  CLUS_3                0                 44
  CLUS_4                1                 44
D30V8, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                0                 64
  CLUS_2                1                 32
  CLUS_3                3                101
D30V9, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                0                 44
  CLUS_2                4                 63
  CLUS_3                1                 35
D30V10, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                3                 63
  CLUS_2                1                 20
  CLUS_3                1                 59

Clustering(31) Variable = 18p gain mutation analysis
D31V1, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                9                163
  CLUS_2               11                159
  CLUS_3                6                161
D31V2, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               15                202
  CLUS_2                3                123
  CLUS_3                8                158
D31V3, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                6                133
  CLUS_2                9                148
  CLUS_3                2                 70
  CLUS_4                8                 96
D31V4, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                7                156
  CLUS_2               13                166
  CLUS_3                5                125
D31V5, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               17                144
  CLUS_2                3                211
  CLUS_3                8                180
D31V6, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                4                 34
  CLUS_2                1                 19
  CLUS_3                1                 23
  CLUS_4                0                 27
D31V7, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                4                 50
  CLUS_2                3                 55
  CLUS_3                2                 42
  CLUS_4                6                 39
D31V8, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                3                 61
  CLUS_2                2                 31
  CLUS_3               10                 94
D31V9, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                2                 42
  CLUS_2                8                 59
  CLUS_3                0                 36
D31V10, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                7                 59
  CLUS_2                1                 20
  CLUS_3                2                 58

Clustering(32) Variable = 18q gain mutation analysis
D32V1, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                9                163
  CLUS_2               14                156
  CLUS_3                5                162
D32V2, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               15                202
  CLUS_2                3                123
  CLUS_3               10                156
D32V3, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                6                133
  CLUS_2               10                147
  CLUS_3                2                 70
  CLUS_4                9                 95
D32V4, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                8                155
  CLUS_2               13                166
  CLUS_3                6                124
D32V5, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               18                143
  CLUS_2                3                211
  CLUS_3                9                179
D32V6, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                4                 34
  CLUS_2                1                 19
  CLUS_3                1                 23
  CLUS_4                0                 27
D32V7, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                4                 50
  CLUS_2                5                 53
  CLUS_3                2                 42
  CLUS_4                5                 40
D32V8, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                3                 61
  CLUS_2                2                 31
  CLUS_3               11                 93
D32V9, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                 43
  CLUS_2                8                 59
  CLUS_3                0                 36
D32V10, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                7                 59
  CLUS_2                1                 20
  CLUS_3                1                 59

Clustering(33) Variable = 19p gain mutation analysis
D33V1, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               46                126
  CLUS_2               23                147
  CLUS_3               88                 79
D33V2, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               64                153
  CLUS_2               66                 60
  CLUS_3               27                139
D33V3, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               52                 87
  CLUS_2               49                108
  CLUS_3               17                 55
  CLUS_4               34                 70
D33V4, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               52                111
  CLUS_2               75                104
  CLUS_3               25                105
D33V5, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               24                137
  CLUS_2              122                 92
  CLUS_3               30                158
D33V6, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                8                 30
  CLUS_2               11                  9
  CLUS_3                8                 16
  CLUS_4                1                 26
D33V7, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               15                 39
  CLUS_2               13                 45
  CLUS_3               22                 22
  CLUS_4               11                 34
D33V8, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               35                 29
  CLUS_2                6                 27
  CLUS_3               20                 84
D33V9, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                7                 37
  CLUS_2               22                 45
  CLUS_3               12                 24
D33V10, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               16                 50
  CLUS_2               12                  9
  CLUS_3               13                 47

Clustering(34) Variable = 19q gain mutation analysis
D34V1, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               41                131
  CLUS_2               14                156
  CLUS_3               79                 88
D34V2, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               57                160
  CLUS_2               60                 66
  CLUS_3               17                149
D34V3, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               48                 91
  CLUS_2               40                117
  CLUS_3               13                 59
  CLUS_4               31                 73
D34V4, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               48                115
  CLUS_2               66                113
  CLUS_3               18                112
D34V5, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               14                147
  CLUS_2              115                 99
  CLUS_3               22                166
D34V6, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                7                 31
  CLUS_2                8                 12
  CLUS_3                7                 17
  CLUS_4                1                 26
D34V7, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               11                 43
  CLUS_2               11                 47
  CLUS_3               18                 26
  CLUS_4                9                 36
D34V8, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               30                 34
  CLUS_2                4                 29
  CLUS_3               15                 89
D34V9, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                5                 39
  CLUS_2               22                 45
  CLUS_3               11                 25
D34V10, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               16                 50
  CLUS_2               11                 10
  CLUS_3               11                 49

Clustering(35) Variable = 20p gain mutation analysis
D35V1, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               41                131
  CLUS_2               27                143
  CLUS_3               88                 79
D35V2, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               59                158
  CLUS_2               70                 56
  CLUS_3               27                139
D35V3, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               44                 95
  CLUS_2               50                107
  CLUS_3               16                 56
  CLUS_4               39                 65
D35V4, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               58                105
  CLUS_2               69                110
  CLUS_3               22                108
D35V5, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               42                119
  CLUS_2              102                112
  CLUS_3               36                152
D35V6, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               13                 25
  CLUS_2                7                 13
  CLUS_3               10                 14
  CLUS_4                3                 24
D35V7, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               14                 40
  CLUS_2               12                 46
  CLUS_3               19                 25
  CLUS_4               14                 31
D35V8, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               29                 35
  CLUS_2                5                 28
  CLUS_3               25                 79
D35V9, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               11                 33
  CLUS_2               19                 48
  CLUS_3                9                 27
D35V10, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               15                 51
  CLUS_2               13                  8
  CLUS_3               11                 49

Clustering(36) Variable = 20q gain mutation analysis
D36V1, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               42                130
  CLUS_2               26                144
  CLUS_3               87                 80
D36V2, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               62                155
  CLUS_2               67                 59
  CLUS_3               26                140
D36V3, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               45                 94
  CLUS_2               50                107
  CLUS_3               15                 57
  CLUS_4               38                 66
D36V4, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               57                106
  CLUS_2               71                108
  CLUS_3               20                110
D36V5, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               40                121
  CLUS_2              101                113
  CLUS_3               37                151
D36V6, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               13                 25
  CLUS_2                7                 13
  CLUS_3               11                 13
  CLUS_4                2                 25
D36V7, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               15                 39
  CLUS_2               11                 47
  CLUS_3               19                 25
  CLUS_4               15                 30
D36V8, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               30                 34
  CLUS_2                5                 28
  CLUS_3               25                 79
D36V9, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               10                 34
  CLUS_2               19                 48
  CLUS_3                9                 27
D36V10, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               15                 51
  CLUS_2               13                  8
  CLUS_3               10                 50

Clustering(37) Variable = 21q gain mutation analysis
D37V1, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               20                152
  CLUS_2                7                163
  CLUS_3                5                162
D37V2, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               21                196
  CLUS_2                5                121
  CLUS_3                6                160
D37V3, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               14                125
  CLUS_2                7                150
  CLUS_3                1                 71
  CLUS_4               13                 91
D37V4, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               21                142
  CLUS_2               11                168
  CLUS_3                3                127
D37V5, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               13                148
  CLUS_2                7                207
  CLUS_3               16                172
D37V6, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                107 
        TCGA-06-0650         TCGA-06-1804         TCGA-06-5408 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-06-5410         TCGA-06-5411         TCGA-06-5412 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-06-5413         TCGA-06-5414         TCGA-06-5415 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-06-5416         TCGA-06-5418         TCGA-06-5856 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-06-5858         TCGA-06-5859         TCGA-06-6388 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-06-6389         TCGA-06-6390         TCGA-06-6391 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-06-6693         TCGA-06-6694         TCGA-06-6695 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-06-6697         TCGA-06-6698         TCGA-06-6699 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-06-6700         TCGA-06-6701         TCGA-12-5295 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-12-5299         TCGA-12-5301         TCGA-14-0740 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-14-0781         TCGA-14-0862         TCGA-14-1043 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-14-1395         TCGA-14-1450         TCGA-15-1444 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-19-4065         TCGA-19-5947         TCGA-19-5950 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-19-5951         TCGA-19-5952         TCGA-19-5953 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-19-5954         TCGA-19-5955         TCGA-19-5956 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-19-5958         TCGA-19-5959         TCGA-19-5960 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-26-1442         TCGA-26-5132         TCGA-26-5133 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-26-5134         TCGA-26-5135         TCGA-26-5136 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-26-5139         TCGA-26-6173         TCGA-26-6174 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-28-2501         TCGA-28-2510         TCGA-28-5204 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-28-5211         TCGA-28-5213         TCGA-28-5214 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-28-5215         TCGA-28-5216         TCGA-28-5219 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-28-5220         TCGA-28-6450         TCGA-32-1979 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-5222         TCGA-41-5651 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-41-6646         TCGA-74-6573         TCGA-74-6575 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-74-6577         TCGA-74-6578         TCGA-74-6581 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-74-6584         TCGA-76-4925         TCGA-76-4926 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-76-4928         TCGA-76-4929         TCGA-76-4931 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-76-4934         TCGA-76-4935         TCGA-76-6191 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-76-6192         TCGA-76-6193         TCGA-76-6280 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-76-6282         TCGA-76-6283         TCGA-76-6285 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-76-6286         TCGA-76-6656         TCGA-76-6657 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-76-6660         TCGA-76-6661         TCGA-76-6662 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-76-6663         TCGA-76-6664         TCGA-81-5910 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-81-5911         TCGA-87-5896 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D37V7, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                5                 49
  CLUS_2                2                 56
  CLUS_3                2                 42
  CLUS_4                1                 44
D37V8, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                3                 61
  CLUS_2                2                 31
  CLUS_3                5                 99
D37V9, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                 44
  CLUS_2                9                 58
  CLUS_3                2                 34
D37V10, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                9                 57
  CLUS_2                1                 20
  CLUS_3                1                 59

Clustering(38) Variable = 22q gain mutation analysis
D38V1, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                4                168
  CLUS_2                6                164
  CLUS_3                0                167
D38V2, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                6                211
  CLUS_2                0                126
  CLUS_3                4                162
D38V3, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                1                138
  CLUS_2                2                155
  CLUS_3                2                 70
  CLUS_4                5                 99
D38V4, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                5                158
  CLUS_2                2                177
  CLUS_3                3                127
D38V5, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                6                155
  CLUS_2                1                213
  CLUS_3                4                184
D38V6, multiclass
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                108 
        TCGA-06-0650         TCGA-06-1804         TCGA-06-1806 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5299         TCGA-12-5301 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-14-0740         TCGA-14-0781         TCGA-14-0862 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-14-1043         TCGA-14-1395         TCGA-14-1450 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-15-1444         TCGA-19-4065         TCGA-19-5947 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-19-5950         TCGA-19-5951         TCGA-19-5952 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-19-5953         TCGA-19-5954         TCGA-19-5955 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-19-5956         TCGA-19-5958         TCGA-19-5959 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-26-5136         TCGA-26-5139         TCGA-26-6173 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-26-6174         TCGA-28-2501         TCGA-28-2510 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5211         TCGA-28-5213 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-5214         TCGA-28-5215         TCGA-28-5216 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-5219         TCGA-28-5220         TCGA-28-6450 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-32-1979         TCGA-32-1980         TCGA-32-5222 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-41-5651         TCGA-41-6646         TCGA-74-6573 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-74-6575         TCGA-74-6577         TCGA-74-6578 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-74-6581         TCGA-74-6584         TCGA-76-4925 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-76-4931         TCGA-76-4934         TCGA-76-4935 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-76-6191         TCGA-76-6192         TCGA-76-6193 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-76-6280         TCGA-76-6282         TCGA-76-6283 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-76-6285         TCGA-76-6286         TCGA-76-6656 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-76-6657         TCGA-76-6660         TCGA-76-6661 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-76-6662         TCGA-76-6663         TCGA-76-6664 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-81-5910         TCGA-81-5911         TCGA-87-5896 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
D38V7, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                1                 53
  CLUS_2                1                 57
  CLUS_3                0                 44
  CLUS_4                1                 44
D38V8, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                0                 64
  CLUS_2                1                 32
  CLUS_3                2                102
D38V9, multiclass
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2570         TCGA-06-5408 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-5410         TCGA-06-5411         TCGA-06-5412 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-5413         TCGA-06-5414         TCGA-06-5415 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-5416         TCGA-06-5418         TCGA-06-5856 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-5858         TCGA-06-5859         TCGA-08-0386 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-12-0616         TCGA-12-0618         TCGA-12-0619 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-12-0821         TCGA-12-3650         TCGA-12-3652 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-12-3653         TCGA-12-5295         TCGA-12-5299 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-14-0781         TCGA-14-0787         TCGA-14-0789 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-14-0790         TCGA-14-0817         TCGA-14-1034 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-14-1823         TCGA-14-1825         TCGA-14-1829 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-14-2554         TCGA-15-0742         TCGA-15-1444 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-16-0846         TCGA-16-1045         TCGA-19-1390 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2620 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-19-2624         TCGA-19-2625         TCGA-19-2629 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-19-4065         TCGA-19-5960         TCGA-26-1442 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-26-5135         TCGA-26-5136         TCGA-26-5139 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-27-1830         TCGA-27-1831         TCGA-27-1832 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1835         TCGA-27-1837 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-27-2519         TCGA-27-2521         TCGA-27-2523 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-27-2524         TCGA-27-2526         TCGA-27-2528 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-1747         TCGA-28-1753         TCGA-28-2509 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-2510         TCGA-28-2513         TCGA-28-2514 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5213         TCGA-28-5215 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-5216         TCGA-28-5220         TCGA-32-1970 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-76-4931 
"22Q GAIN WILD-TYPE" 
D38V10, multiclass
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2570         TCGA-06-5408 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-5410         TCGA-06-5411         TCGA-06-5412 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-5413         TCGA-06-5414         TCGA-06-5415 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-5416         TCGA-06-5418         TCGA-06-5856 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-06-5858         TCGA-06-5859         TCGA-08-0386 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-12-0616         TCGA-12-0618         TCGA-12-0619 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-12-0821         TCGA-12-3650         TCGA-12-3652 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-12-3653         TCGA-12-5295         TCGA-12-5299 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-14-0781         TCGA-14-0787         TCGA-14-0789 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-14-0790         TCGA-14-0817         TCGA-14-1034 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-14-1823         TCGA-14-1825         TCGA-14-1829 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-14-2554         TCGA-15-0742         TCGA-15-1444 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-16-0846         TCGA-16-1045         TCGA-19-1390 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2620 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-19-2624         TCGA-19-2625         TCGA-19-2629 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-19-4065         TCGA-19-5960         TCGA-26-1442 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-26-5132         TCGA-26-5133         TCGA-26-5134 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-26-5135         TCGA-26-5136         TCGA-26-5139 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-27-1830         TCGA-27-1831         TCGA-27-1832 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-27-1834         TCGA-27-1835         TCGA-27-1837 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-27-2519         TCGA-27-2521         TCGA-27-2523 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-27-2524         TCGA-27-2526         TCGA-27-2528 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-1747         TCGA-28-1753         TCGA-28-2509 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-2510         TCGA-28-2513         TCGA-28-2514 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5213         TCGA-28-5215 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-28-5216         TCGA-28-5220         TCGA-32-1970 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-76-4931 
"22Q GAIN WILD-TYPE" 

Clustering(39) Variable = Xq gain mutation analysis
D39V1, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               3               169
  CLUS_2               1               169
  CLUS_3               0               167
D39V2, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               3               214
  CLUS_2               0               126
  CLUS_3               1               165
D39V3, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1               138
  CLUS_2               2               155
  CLUS_3               1                71
  CLUS_4               0               104
D39V4, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0               163
  CLUS_2               3               176
  CLUS_3               1               129
D39V5, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               3               158
  CLUS_2               0               214
  CLUS_3               1               187
D39V6, multiclass
D39V7, multiclass
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1               200 
       TCGA-02-0003        TCGA-02-0011        TCGA-02-0014        TCGA-02-0068 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-02-0069        TCGA-02-0116        TCGA-02-2470        TCGA-02-2485 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0125        TCGA-06-0126        TCGA-06-0128        TCGA-06-0129 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0130        TCGA-06-0154        TCGA-06-0155        TCGA-06-0171 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0189        TCGA-06-0238        TCGA-06-0644        TCGA-06-0650 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0875        TCGA-06-0876        TCGA-06-0877        TCGA-06-0878 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0879        TCGA-06-0882        TCGA-06-0939        TCGA-06-1084 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-1086        TCGA-06-1087        TCGA-06-1800        TCGA-06-1802 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-1804        TCGA-06-1805        TCGA-06-1806        TCGA-06-2557 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-2558        TCGA-06-2559        TCGA-06-2562        TCGA-06-2563 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-2564        TCGA-06-2565        TCGA-06-2566        TCGA-06-2567 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-2570        TCGA-06-5408        TCGA-06-5410        TCGA-06-5411 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-5412        TCGA-06-5413        TCGA-06-5414        TCGA-06-5415 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-5416        TCGA-06-5418        TCGA-06-5856        TCGA-06-5858 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-5859        TCGA-06-6388        TCGA-06-6389        TCGA-06-6390 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-6391        TCGA-06-6693        TCGA-06-6694        TCGA-06-6695 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-6697        TCGA-06-6698        TCGA-06-6699        TCGA-06-6700 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-6701        TCGA-08-0245        TCGA-08-0344        TCGA-08-0345 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-08-0346        TCGA-08-0347        TCGA-08-0348        TCGA-08-0349 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-08-0350        TCGA-08-0351        TCGA-08-0352        TCGA-08-0353 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-08-0354        TCGA-08-0355        TCGA-08-0356        TCGA-08-0357 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-08-0358        TCGA-08-0359        TCGA-08-0375        TCGA-08-0380 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-08-0386        TCGA-08-0389        TCGA-08-0390        TCGA-08-0392 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-12-0691        TCGA-12-0692        TCGA-12-1598        TCGA-12-1599 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-12-3646        TCGA-12-3649        TCGA-12-3650        TCGA-12-3651 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-12-3652        TCGA-12-3653        TCGA-12-5295        TCGA-12-5301 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-14-0813        TCGA-14-0862        TCGA-14-0871        TCGA-14-1823 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-15-1446        TCGA-15-1447        TCGA-15-1449        TCGA-16-0846 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-16-1460        TCGA-19-0957        TCGA-19-0962        TCGA-19-1386 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-1389        TCGA-19-1390        TCGA-19-1392        TCGA-19-1786 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-1789        TCGA-19-1791        TCGA-19-2619        TCGA-19-2620 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-2625        TCGA-19-2631        TCGA-19-5947        TCGA-19-5950 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-5951        TCGA-19-5952        TCGA-19-5953        TCGA-19-5954 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-5955        TCGA-19-5956        TCGA-19-5958        TCGA-19-5959 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-5960        TCGA-26-1440        TCGA-26-1442        TCGA-26-5132 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-26-5133        TCGA-26-5134        TCGA-26-6173        TCGA-26-6174 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-27-1830        TCGA-27-1831        TCGA-27-1832        TCGA-27-1833 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-27-1834        TCGA-27-1836        TCGA-27-2518        TCGA-27-2528 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-1746        TCGA-28-1747        TCGA-28-1750        TCGA-28-1752 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-1753        TCGA-28-1757        TCGA-28-2501        TCGA-28-5208 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-5214        TCGA-32-1970        TCGA-32-1976        TCGA-32-1978 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-32-1982        TCGA-32-1986        TCGA-32-1987        TCGA-32-1991 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-32-4211        TCGA-32-5222        TCGA-41-2573        TCGA-41-2575 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-41-3392        TCGA-41-3393        TCGA-41-3915        TCGA-41-4097 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-41-5651        TCGA-41-6646        TCGA-74-6573        TCGA-74-6575 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-74-6577        TCGA-74-6578        TCGA-74-6581        TCGA-74-6584 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-76-4926        TCGA-76-4928        TCGA-76-4929        TCGA-76-4931 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-76-6192        TCGA-76-6193        TCGA-76-6282        TCGA-76-6283 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-76-6285        TCGA-76-6656        TCGA-76-6657        TCGA-76-6660 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-76-6662        TCGA-76-6663        TCGA-76-6664        TCGA-81-5910 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D39V8, multiclass
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1               200 
       TCGA-02-0003        TCGA-02-0011        TCGA-02-0014        TCGA-02-0068 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-02-0069        TCGA-02-0116        TCGA-02-2470        TCGA-02-2485 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0125        TCGA-06-0126        TCGA-06-0128        TCGA-06-0129 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0130        TCGA-06-0154        TCGA-06-0155        TCGA-06-0171 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0189        TCGA-06-0238        TCGA-06-0644        TCGA-06-0650 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0875        TCGA-06-0876        TCGA-06-0877        TCGA-06-0878 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0879        TCGA-06-0882        TCGA-06-0939        TCGA-06-1084 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-1086        TCGA-06-1087        TCGA-06-1800        TCGA-06-1802 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-1804        TCGA-06-1805        TCGA-06-1806        TCGA-06-2557 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-2558        TCGA-06-2559        TCGA-06-2562        TCGA-06-2563 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-2564        TCGA-06-2565        TCGA-06-2566        TCGA-06-2567 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-2570        TCGA-06-5408        TCGA-06-5410        TCGA-06-5411 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-5412        TCGA-06-5413        TCGA-06-5414        TCGA-06-5415 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-5416        TCGA-06-5418        TCGA-06-5856        TCGA-06-5858 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-5859        TCGA-06-6388        TCGA-06-6389        TCGA-06-6390 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-6391        TCGA-06-6693        TCGA-06-6694        TCGA-06-6695 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-6697        TCGA-06-6698        TCGA-06-6699        TCGA-06-6700 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-6701        TCGA-08-0245        TCGA-08-0344        TCGA-08-0345 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-08-0346        TCGA-08-0347        TCGA-08-0348        TCGA-08-0349 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-08-0350        TCGA-08-0351        TCGA-08-0352        TCGA-08-0353 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-08-0354        TCGA-08-0355        TCGA-08-0356        TCGA-08-0357 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-08-0358        TCGA-08-0359        TCGA-08-0375        TCGA-08-0380 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-08-0386        TCGA-08-0389        TCGA-08-0390        TCGA-08-0392 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-12-0691        TCGA-12-0692        TCGA-12-1598        TCGA-12-1599 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-12-3646        TCGA-12-3649        TCGA-12-3650        TCGA-12-3651 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-12-3652        TCGA-12-3653        TCGA-12-5295        TCGA-12-5301 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-14-0813        TCGA-14-0862        TCGA-14-0871        TCGA-14-1823 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-15-1446        TCGA-15-1447        TCGA-15-1449        TCGA-16-0846 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-16-1460        TCGA-19-0957        TCGA-19-0962        TCGA-19-1386 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-1389        TCGA-19-1390        TCGA-19-1392        TCGA-19-1786 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-1789        TCGA-19-1791        TCGA-19-2619        TCGA-19-2620 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-2625        TCGA-19-2631        TCGA-19-5947        TCGA-19-5950 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-5951        TCGA-19-5952        TCGA-19-5953        TCGA-19-5954 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-5955        TCGA-19-5956        TCGA-19-5958        TCGA-19-5959 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-5960        TCGA-26-1440        TCGA-26-1442        TCGA-26-5132 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-26-5133        TCGA-26-5134        TCGA-26-6173        TCGA-26-6174 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-27-1830        TCGA-27-1831        TCGA-27-1832        TCGA-27-1833 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-27-1834        TCGA-27-1836        TCGA-27-2518        TCGA-27-2528 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-1746        TCGA-28-1747        TCGA-28-1750        TCGA-28-1752 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-1753        TCGA-28-1757        TCGA-28-2501        TCGA-28-5208 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-5214        TCGA-32-1970        TCGA-32-1976        TCGA-32-1978 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-32-1982        TCGA-32-1986        TCGA-32-1987        TCGA-32-1991 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-32-4211        TCGA-32-5222        TCGA-41-2573        TCGA-41-2575 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-41-3392        TCGA-41-3393        TCGA-41-3915        TCGA-41-4097 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-41-5651        TCGA-41-6646        TCGA-74-6573        TCGA-74-6575 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-74-6577        TCGA-74-6578        TCGA-74-6581        TCGA-74-6584 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-76-4926        TCGA-76-4928        TCGA-76-4929        TCGA-76-4931 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-76-6192        TCGA-76-6193        TCGA-76-6282        TCGA-76-6283 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-76-6285        TCGA-76-6656        TCGA-76-6657        TCGA-76-6660 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-76-6662        TCGA-76-6663        TCGA-76-6664        TCGA-81-5910 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D39V9, multiclass
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1               146 
       TCGA-02-0047        TCGA-02-0055        TCGA-02-2483        TCGA-02-2485 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-02-2486        TCGA-06-0125        TCGA-06-0129        TCGA-06-0130 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0132        TCGA-06-0138        TCGA-06-0141        TCGA-06-0157 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0158        TCGA-06-0168        TCGA-06-0174        TCGA-06-0178 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0184        TCGA-06-0187        TCGA-06-0190        TCGA-06-0210 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0211        TCGA-06-0219        TCGA-06-0238        TCGA-06-0644 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0645        TCGA-06-0646        TCGA-06-0649        TCGA-06-0686 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0743        TCGA-06-0744        TCGA-06-0745        TCGA-06-0747 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0749        TCGA-06-0750        TCGA-06-0878        TCGA-06-0882 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-1804        TCGA-06-2557        TCGA-06-2558        TCGA-06-2559 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-2561        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2567        TCGA-06-2569        TCGA-06-2570 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-5408        TCGA-06-5410        TCGA-06-5411        TCGA-06-5412 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-5413        TCGA-06-5414        TCGA-06-5415        TCGA-06-5416 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-5418        TCGA-06-5856        TCGA-06-5858        TCGA-06-5859 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-08-0386        TCGA-12-0616        TCGA-12-0618        TCGA-12-0619 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-12-0821        TCGA-12-3650        TCGA-12-3652        TCGA-12-3653 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-12-5295        TCGA-12-5299        TCGA-14-0781        TCGA-14-0787 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-14-0789        TCGA-14-0790        TCGA-14-0817        TCGA-14-1034 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-14-1823        TCGA-14-1825        TCGA-14-1829        TCGA-14-2554 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-15-0742        TCGA-15-1444        TCGA-16-0846        TCGA-16-1045 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-1390        TCGA-19-2619        TCGA-19-2620        TCGA-19-2624 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-2625        TCGA-19-2629        TCGA-19-4065        TCGA-19-5960 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-27-1830 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-27-1831        TCGA-27-1832        TCGA-27-1834        TCGA-27-1835 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-27-1837        TCGA-27-2519        TCGA-27-2521        TCGA-27-2523 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-27-2524        TCGA-27-2526        TCGA-27-2528        TCGA-28-1747 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-1753        TCGA-28-2509        TCGA-28-2510        TCGA-28-2513 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-2514        TCGA-28-5204        TCGA-28-5207        TCGA-28-5208 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-5209        TCGA-28-5213        TCGA-28-5215        TCGA-28-5216 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5220        TCGA-32-1970        TCGA-32-1980 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-32-1982        TCGA-32-2615        TCGA-32-2616        TCGA-32-2632 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-32-2634        TCGA-32-2638        TCGA-32-4213        TCGA-32-5222 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-41-2571        TCGA-41-2572        TCGA-41-3915        TCGA-41-4097 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-41-5651        TCGA-76-4925        TCGA-76-4926        TCGA-76-4928 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-76-4929        TCGA-76-4931 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D39V10, multiclass
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1               146 
       TCGA-02-0047        TCGA-02-0055        TCGA-02-2483        TCGA-02-2485 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-02-2486        TCGA-06-0125        TCGA-06-0129        TCGA-06-0130 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0132        TCGA-06-0138        TCGA-06-0141        TCGA-06-0157 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0158        TCGA-06-0168        TCGA-06-0174        TCGA-06-0178 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0184        TCGA-06-0187        TCGA-06-0190        TCGA-06-0210 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0211        TCGA-06-0219        TCGA-06-0238        TCGA-06-0644 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0645        TCGA-06-0646        TCGA-06-0649        TCGA-06-0686 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0743        TCGA-06-0744        TCGA-06-0745        TCGA-06-0747 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-0749        TCGA-06-0750        TCGA-06-0878        TCGA-06-0882 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-1804        TCGA-06-2557        TCGA-06-2558        TCGA-06-2559 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-2561        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2567        TCGA-06-2569        TCGA-06-2570 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-5408        TCGA-06-5410        TCGA-06-5411        TCGA-06-5412 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-5413        TCGA-06-5414        TCGA-06-5415        TCGA-06-5416 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-06-5418        TCGA-06-5856        TCGA-06-5858        TCGA-06-5859 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-08-0386        TCGA-12-0616        TCGA-12-0618        TCGA-12-0619 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-12-0821        TCGA-12-3650        TCGA-12-3652        TCGA-12-3653 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-12-5295        TCGA-12-5299        TCGA-14-0781        TCGA-14-0787 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-14-0789        TCGA-14-0790        TCGA-14-0817        TCGA-14-1034 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-14-1823        TCGA-14-1825        TCGA-14-1829        TCGA-14-2554 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-15-0742        TCGA-15-1444        TCGA-16-0846        TCGA-16-1045 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-1390        TCGA-19-2619        TCGA-19-2620        TCGA-19-2624 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-19-2625        TCGA-19-2629        TCGA-19-4065        TCGA-19-5960 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-27-1830 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-27-1831        TCGA-27-1832        TCGA-27-1834        TCGA-27-1835 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-27-1837        TCGA-27-2519        TCGA-27-2521        TCGA-27-2523 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-27-2524        TCGA-27-2526        TCGA-27-2528        TCGA-28-1747 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-1753        TCGA-28-2509        TCGA-28-2510        TCGA-28-2513 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-2514        TCGA-28-5204        TCGA-28-5207        TCGA-28-5208 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-5209        TCGA-28-5213        TCGA-28-5215        TCGA-28-5216 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5220        TCGA-32-1970        TCGA-32-1980 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-32-1982        TCGA-32-2615        TCGA-32-2616        TCGA-32-2632 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-32-2634        TCGA-32-2638        TCGA-32-4213        TCGA-32-5222 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-41-2571        TCGA-41-2572        TCGA-41-3915        TCGA-41-4097 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-41-5651        TCGA-76-4925        TCGA-76-4926        TCGA-76-4928 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-76-4929        TCGA-76-4931 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 

Clustering(40) Variable = 1p loss mutation analysis
D40V1, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1               171
  CLUS_2               2               168
  CLUS_3               1               166
D40V2, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1               216
  CLUS_2               1               125
  CLUS_3               2               164
D40V3, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1               138
  CLUS_2               2               155
  CLUS_3               0                72
  CLUS_4               1               103
D40V4, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               0               163
  CLUS_2               1               178
  CLUS_3               3               127
D40V5, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1               160
  CLUS_2               1               213
  CLUS_3               3               185
D40V6, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                1               108 
       TCGA-06-0650        TCGA-06-1804        TCGA-06-1806        TCGA-06-5408 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-06-6388 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-6389        TCGA-06-6390        TCGA-06-6391        TCGA-06-6693 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-6694        TCGA-06-6695        TCGA-06-6697        TCGA-06-6698 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-6699        TCGA-06-6700        TCGA-06-6701        TCGA-12-5295 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-12-5299        TCGA-12-5301        TCGA-14-0781        TCGA-14-0862 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-14-1043        TCGA-14-1395        TCGA-14-1450        TCGA-15-1444 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-4065        TCGA-19-5947        TCGA-19-5950        TCGA-19-5951 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-5952        TCGA-19-5953        TCGA-19-5954        TCGA-19-5955 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-5956        TCGA-19-5958        TCGA-19-5959        TCGA-19-5960 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-26-6173 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-26-6174        TCGA-28-2501        TCGA-28-2510        TCGA-28-5204 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-5207        TCGA-28-5208        TCGA-28-5209        TCGA-28-5211 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-5213        TCGA-28-5214        TCGA-28-5215        TCGA-28-5216 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5219        TCGA-28-5220        TCGA-28-6450 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-32-1979        TCGA-32-1980        TCGA-32-5222        TCGA-41-5651 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4925 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-4926        TCGA-76-4928        TCGA-76-4929        TCGA-76-4931 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-4934        TCGA-76-4935        TCGA-76-6191        TCGA-76-6192 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-6193        TCGA-76-6280        TCGA-76-6282        TCGA-76-6283 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-6285        TCGA-76-6286        TCGA-76-6656        TCGA-76-6657 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-6660        TCGA-76-6661        TCGA-76-6662        TCGA-76-6663 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-6664        TCGA-81-5910        TCGA-81-5911        TCGA-87-5896 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D40V7, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2               199 
       TCGA-02-0003        TCGA-02-0011        TCGA-02-0014        TCGA-02-0068 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-02-0069        TCGA-02-0116        TCGA-02-2470        TCGA-02-2485 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0125        TCGA-06-0126        TCGA-06-0128        TCGA-06-0129 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0130        TCGA-06-0154        TCGA-06-0155        TCGA-06-0171 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0189        TCGA-06-0238        TCGA-06-0644        TCGA-06-0650 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0875        TCGA-06-0876        TCGA-06-0877        TCGA-06-0878 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0879        TCGA-06-0882        TCGA-06-0939        TCGA-06-1084 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-1086        TCGA-06-1087        TCGA-06-1800        TCGA-06-1802 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-1804        TCGA-06-1805        TCGA-06-1806        TCGA-06-2557 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-2558        TCGA-06-2559        TCGA-06-2562        TCGA-06-2563 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-2564        TCGA-06-2565        TCGA-06-2566        TCGA-06-2567 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-2570        TCGA-06-5408        TCGA-06-5410        TCGA-06-5411 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5412        TCGA-06-5413        TCGA-06-5414        TCGA-06-5415 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5416        TCGA-06-5418        TCGA-06-5856        TCGA-06-5858 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5859        TCGA-06-6388        TCGA-06-6389        TCGA-06-6390 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-6391        TCGA-06-6693        TCGA-06-6694        TCGA-06-6695 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-6697        TCGA-06-6698        TCGA-06-6699        TCGA-06-6700 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-6701        TCGA-08-0245        TCGA-08-0345        TCGA-08-0346 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-08-0347        TCGA-08-0348        TCGA-08-0349        TCGA-08-0350 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-08-0351        TCGA-08-0352        TCGA-08-0353        TCGA-08-0354 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-08-0355        TCGA-08-0356        TCGA-08-0357        TCGA-08-0358 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-08-0359        TCGA-08-0375        TCGA-08-0380        TCGA-08-0386 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-08-0389        TCGA-08-0390        TCGA-08-0392        TCGA-12-0691 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-12-0692        TCGA-12-1598        TCGA-12-1599        TCGA-12-3646 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-12-3649        TCGA-12-3650        TCGA-12-3651        TCGA-12-3652 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-12-3653        TCGA-12-5295        TCGA-12-5301        TCGA-14-0813 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-14-0862        TCGA-14-0871        TCGA-14-1823        TCGA-15-1446 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-15-1447        TCGA-15-1449        TCGA-16-0846        TCGA-16-1460 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-0957        TCGA-19-0962        TCGA-19-1386        TCGA-19-1389 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-1392        TCGA-19-1786        TCGA-19-1789        TCGA-19-1791 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-2619        TCGA-19-2620        TCGA-19-2625        TCGA-19-2631 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-5947        TCGA-19-5950        TCGA-19-5951        TCGA-19-5952 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-5953        TCGA-19-5954        TCGA-19-5955        TCGA-19-5956 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-5958        TCGA-19-5959        TCGA-19-5960        TCGA-26-1440 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-26-6173        TCGA-26-6174        TCGA-27-1830        TCGA-27-1831 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-27-1832        TCGA-27-1833        TCGA-27-1834        TCGA-27-1836 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-27-2518        TCGA-27-2528        TCGA-28-1746        TCGA-28-1747 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-1750        TCGA-28-1752        TCGA-28-1753        TCGA-28-1757 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-2501        TCGA-28-5208        TCGA-28-5214        TCGA-32-1970 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-32-1976        TCGA-32-1978        TCGA-32-1982        TCGA-32-1986 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-32-1987        TCGA-32-1991        TCGA-32-4210        TCGA-32-4211 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-32-5222        TCGA-41-2573        TCGA-41-2575        TCGA-41-3392 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-41-3393        TCGA-41-3915        TCGA-41-4097        TCGA-41-5651 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4926 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-6192 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-6193        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-6656        TCGA-76-6657        TCGA-76-6660        TCGA-76-6662 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-6663        TCGA-76-6664        TCGA-81-5910 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D40V8, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2               199 
       TCGA-02-0003        TCGA-02-0011        TCGA-02-0014        TCGA-02-0068 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-02-0069        TCGA-02-0116        TCGA-02-2470        TCGA-02-2485 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0125        TCGA-06-0126        TCGA-06-0128        TCGA-06-0129 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0130        TCGA-06-0154        TCGA-06-0155        TCGA-06-0171 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0189        TCGA-06-0238        TCGA-06-0644        TCGA-06-0650 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0875        TCGA-06-0876        TCGA-06-0877        TCGA-06-0878 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0879        TCGA-06-0882        TCGA-06-0939        TCGA-06-1084 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-1086        TCGA-06-1087        TCGA-06-1800        TCGA-06-1802 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-1804        TCGA-06-1805        TCGA-06-1806        TCGA-06-2557 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-2558        TCGA-06-2559        TCGA-06-2562        TCGA-06-2563 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-2564        TCGA-06-2565        TCGA-06-2566        TCGA-06-2567 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-2570        TCGA-06-5408        TCGA-06-5410        TCGA-06-5411 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5412        TCGA-06-5413        TCGA-06-5414        TCGA-06-5415 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5416        TCGA-06-5418        TCGA-06-5856        TCGA-06-5858 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5859        TCGA-06-6388        TCGA-06-6389        TCGA-06-6390 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-6391        TCGA-06-6693        TCGA-06-6694        TCGA-06-6695 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-6697        TCGA-06-6698        TCGA-06-6699        TCGA-06-6700 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-6701        TCGA-08-0245        TCGA-08-0345        TCGA-08-0346 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-08-0347        TCGA-08-0348        TCGA-08-0349        TCGA-08-0350 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-08-0351        TCGA-08-0352        TCGA-08-0353        TCGA-08-0354 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-08-0355        TCGA-08-0356        TCGA-08-0357        TCGA-08-0358 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-08-0359        TCGA-08-0375        TCGA-08-0380        TCGA-08-0386 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-08-0389        TCGA-08-0390        TCGA-08-0392        TCGA-12-0691 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-12-0692        TCGA-12-1598        TCGA-12-1599        TCGA-12-3646 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-12-3649        TCGA-12-3650        TCGA-12-3651        TCGA-12-3652 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-12-3653        TCGA-12-5295        TCGA-12-5301        TCGA-14-0813 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-14-0862        TCGA-14-0871        TCGA-14-1823        TCGA-15-1446 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-15-1447        TCGA-15-1449        TCGA-16-0846        TCGA-16-1460 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-0957        TCGA-19-0962        TCGA-19-1386        TCGA-19-1389 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-1392        TCGA-19-1786        TCGA-19-1789        TCGA-19-1791 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-2619        TCGA-19-2620        TCGA-19-2625        TCGA-19-2631 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-5947        TCGA-19-5950        TCGA-19-5951        TCGA-19-5952 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-5953        TCGA-19-5954        TCGA-19-5955        TCGA-19-5956 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-5958        TCGA-19-5959        TCGA-19-5960        TCGA-26-1440 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-26-6173        TCGA-26-6174        TCGA-27-1830        TCGA-27-1831 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-27-1832        TCGA-27-1833        TCGA-27-1834        TCGA-27-1836 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-27-2518        TCGA-27-2528        TCGA-28-1746        TCGA-28-1747 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-1750        TCGA-28-1752        TCGA-28-1753        TCGA-28-1757 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-2501        TCGA-28-5208        TCGA-28-5214        TCGA-32-1970 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-32-1976        TCGA-32-1978        TCGA-32-1982        TCGA-32-1986 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-32-1987        TCGA-32-1991        TCGA-32-4210        TCGA-32-4211 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-32-5222        TCGA-41-2573        TCGA-41-2575        TCGA-41-3392 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-41-3393        TCGA-41-3915        TCGA-41-4097        TCGA-41-5651 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4926 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-6192 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-6193        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-6656        TCGA-76-6657        TCGA-76-6660        TCGA-76-6662 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-6663        TCGA-76-6664        TCGA-81-5910 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D40V9, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                1               146 
       TCGA-02-0047        TCGA-02-0055        TCGA-02-2483        TCGA-02-2485 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-02-2486        TCGA-06-0125        TCGA-06-0129        TCGA-06-0130 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0132        TCGA-06-0138        TCGA-06-0141        TCGA-06-0157 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0158        TCGA-06-0168        TCGA-06-0174        TCGA-06-0178 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0184        TCGA-06-0187        TCGA-06-0190        TCGA-06-0210 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0211        TCGA-06-0219        TCGA-06-0238        TCGA-06-0644 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0645        TCGA-06-0646        TCGA-06-0649        TCGA-06-0686 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0743        TCGA-06-0744        TCGA-06-0745        TCGA-06-0747 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0749        TCGA-06-0750        TCGA-06-0878        TCGA-06-0882 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-1804        TCGA-06-2557        TCGA-06-2558        TCGA-06-2559 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-2561        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2567        TCGA-06-2569        TCGA-06-2570 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5408        TCGA-06-5410        TCGA-06-5411        TCGA-06-5412 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5413        TCGA-06-5414        TCGA-06-5415        TCGA-06-5416 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5418        TCGA-06-5856        TCGA-06-5858        TCGA-06-5859 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-08-0386        TCGA-12-0616        TCGA-12-0618        TCGA-12-0619 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-12-0821        TCGA-12-3650        TCGA-12-3652        TCGA-12-3653 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-12-5295        TCGA-12-5299        TCGA-14-0781        TCGA-14-0787 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-14-0789        TCGA-14-0790        TCGA-14-0817        TCGA-14-1034 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-14-1823        TCGA-14-1825        TCGA-14-1829        TCGA-14-2554 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-15-0742        TCGA-15-1444        TCGA-16-0846        TCGA-16-1045 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-1787        TCGA-19-2619        TCGA-19-2620        TCGA-19-2624 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-2625        TCGA-19-2629        TCGA-19-4065        TCGA-19-5960 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-27-1830 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-27-1831        TCGA-27-1832        TCGA-27-1834        TCGA-27-1835 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-27-1837        TCGA-27-2519        TCGA-27-2521        TCGA-27-2523 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-27-2524        TCGA-27-2526        TCGA-27-2528        TCGA-28-1747 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-1753        TCGA-28-2509        TCGA-28-2510        TCGA-28-2513 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-2514        TCGA-28-5204        TCGA-28-5207        TCGA-28-5208 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-5209        TCGA-28-5213        TCGA-28-5215        TCGA-28-5216 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5220        TCGA-32-1970        TCGA-32-1980 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-32-1982        TCGA-32-2615        TCGA-32-2616        TCGA-32-2632 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-32-2634        TCGA-32-2638        TCGA-32-4213        TCGA-32-5222 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-41-2571        TCGA-41-2572        TCGA-41-3915        TCGA-41-4097 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-41-5651        TCGA-76-4925        TCGA-76-4926        TCGA-76-4928 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-4929        TCGA-76-4931 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D40V10, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                1               146 
       TCGA-02-0047        TCGA-02-0055        TCGA-02-2483        TCGA-02-2485 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-02-2486        TCGA-06-0125        TCGA-06-0129        TCGA-06-0130 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0132        TCGA-06-0138        TCGA-06-0141        TCGA-06-0157 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0158        TCGA-06-0168        TCGA-06-0174        TCGA-06-0178 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0184        TCGA-06-0187        TCGA-06-0190        TCGA-06-0210 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0211        TCGA-06-0219        TCGA-06-0238        TCGA-06-0644 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0645        TCGA-06-0646        TCGA-06-0649        TCGA-06-0686 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0743        TCGA-06-0744        TCGA-06-0745        TCGA-06-0747 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-0749        TCGA-06-0750        TCGA-06-0878        TCGA-06-0882 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-1804        TCGA-06-2557        TCGA-06-2558        TCGA-06-2559 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-2561        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2567        TCGA-06-2569        TCGA-06-2570 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5408        TCGA-06-5410        TCGA-06-5411        TCGA-06-5412 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5413        TCGA-06-5414        TCGA-06-5415        TCGA-06-5416 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-06-5418        TCGA-06-5856        TCGA-06-5858        TCGA-06-5859 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-08-0386        TCGA-12-0616        TCGA-12-0618        TCGA-12-0619 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-12-0821        TCGA-12-3650        TCGA-12-3652        TCGA-12-3653 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-12-5295        TCGA-12-5299        TCGA-14-0781        TCGA-14-0787 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-14-0789        TCGA-14-0790        TCGA-14-0817        TCGA-14-1034 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-14-1823        TCGA-14-1825        TCGA-14-1829        TCGA-14-2554 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-15-0742        TCGA-15-1444        TCGA-16-0846        TCGA-16-1045 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-1787        TCGA-19-2619        TCGA-19-2620        TCGA-19-2624 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-19-2625        TCGA-19-2629        TCGA-19-4065        TCGA-19-5960 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-27-1830 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-27-1831        TCGA-27-1832        TCGA-27-1834        TCGA-27-1835 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-27-1837        TCGA-27-2519        TCGA-27-2521        TCGA-27-2523 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-27-2524        TCGA-27-2526        TCGA-27-2528        TCGA-28-1747 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-1753        TCGA-28-2509        TCGA-28-2510        TCGA-28-2513 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-2514        TCGA-28-5204        TCGA-28-5207        TCGA-28-5208 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-5209        TCGA-28-5213        TCGA-28-5215        TCGA-28-5216 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5220        TCGA-32-1970        TCGA-32-1980 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-32-1982        TCGA-32-2615        TCGA-32-2616        TCGA-32-2632 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-32-2634        TCGA-32-2638        TCGA-32-4213        TCGA-32-5222 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-41-2571        TCGA-41-2572        TCGA-41-3915        TCGA-41-4097 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-41-5651        TCGA-76-4925        TCGA-76-4926        TCGA-76-4928 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-76-4929        TCGA-76-4931 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 

Clustering(41) Variable = 1q loss mutation analysis
D41V1, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               0               172
  CLUS_2               1               169
  CLUS_3               2               165
D41V2, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               1               216
  CLUS_2               1               125
  CLUS_3               1               165
D41V3, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               2               137
  CLUS_2               1               156
  CLUS_3               0                72
  CLUS_4               0               104
D41V4, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               1               162
  CLUS_2               1               178
  CLUS_3               1               129
D41V5, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               1               160
  CLUS_2               2               212
  CLUS_3               1               187
D41V6, multiclass
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                1               108 
       TCGA-06-0650        TCGA-06-1804        TCGA-06-1806        TCGA-06-5408 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-06-6388 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-6389        TCGA-06-6390        TCGA-06-6391        TCGA-06-6693 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-6694        TCGA-06-6695        TCGA-06-6697        TCGA-06-6698 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-6699        TCGA-06-6700        TCGA-06-6701        TCGA-12-5295 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-12-5299        TCGA-12-5301        TCGA-14-0781        TCGA-14-0862 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-14-1043        TCGA-14-1395        TCGA-14-1450        TCGA-15-1444 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-4065        TCGA-19-5947        TCGA-19-5950        TCGA-19-5951 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-5952        TCGA-19-5953        TCGA-19-5954        TCGA-19-5955 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-5956        TCGA-19-5958        TCGA-19-5959        TCGA-19-5960 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-26-6173 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-26-6174        TCGA-28-2501        TCGA-28-2510        TCGA-28-5204 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-5207        TCGA-28-5208        TCGA-28-5209        TCGA-28-5211 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-5213        TCGA-28-5214        TCGA-28-5215        TCGA-28-5216 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5219        TCGA-28-5220        TCGA-28-6450 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-32-1979        TCGA-32-1980        TCGA-32-5222        TCGA-41-5651 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4925 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-4926        TCGA-76-4928        TCGA-76-4929        TCGA-76-4931 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-4934        TCGA-76-4935        TCGA-76-6191        TCGA-76-6192 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-6193        TCGA-76-6280        TCGA-76-6282        TCGA-76-6283 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-6285        TCGA-76-6286        TCGA-76-6656        TCGA-76-6657 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-6660        TCGA-76-6661        TCGA-76-6662        TCGA-76-6663 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-6664        TCGA-81-5910        TCGA-81-5911        TCGA-87-5896 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
D41V7, multiclass
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                1               200 
       TCGA-02-0003        TCGA-02-0011        TCGA-02-0014        TCGA-02-0068 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-02-0069        TCGA-02-0116        TCGA-02-2470        TCGA-02-2485 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0125        TCGA-06-0126        TCGA-06-0128        TCGA-06-0129 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0130        TCGA-06-0154        TCGA-06-0155        TCGA-06-0171 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0189        TCGA-06-0238        TCGA-06-0644        TCGA-06-0650 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0875        TCGA-06-0876        TCGA-06-0877        TCGA-06-0878 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0879        TCGA-06-0882        TCGA-06-0939        TCGA-06-1084 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-1086        TCGA-06-1087        TCGA-06-1800        TCGA-06-1802 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-1804        TCGA-06-1805        TCGA-06-1806        TCGA-06-2557 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-2558        TCGA-06-2559        TCGA-06-2562        TCGA-06-2563 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-2564        TCGA-06-2565        TCGA-06-2566        TCGA-06-2567 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-2570        TCGA-06-5408        TCGA-06-5410        TCGA-06-5411 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5412        TCGA-06-5413        TCGA-06-5414        TCGA-06-5415 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5416        TCGA-06-5418        TCGA-06-5856        TCGA-06-5858 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5859        TCGA-06-6388        TCGA-06-6389        TCGA-06-6390 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-6391        TCGA-06-6693        TCGA-06-6694        TCGA-06-6695 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-6697        TCGA-06-6698        TCGA-06-6699        TCGA-06-6700 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-6701        TCGA-08-0245        TCGA-08-0344        TCGA-08-0345 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-08-0346        TCGA-08-0347        TCGA-08-0348        TCGA-08-0349 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-08-0350        TCGA-08-0351        TCGA-08-0352        TCGA-08-0353 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-08-0354        TCGA-08-0355        TCGA-08-0356        TCGA-08-0357 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-08-0358        TCGA-08-0359        TCGA-08-0375        TCGA-08-0380 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-08-0386        TCGA-08-0389        TCGA-08-0390        TCGA-08-0392 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-12-0691        TCGA-12-0692        TCGA-12-1598        TCGA-12-1599 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-12-3646        TCGA-12-3649        TCGA-12-3650        TCGA-12-3651 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-12-3652        TCGA-12-3653        TCGA-12-5295        TCGA-12-5301 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-14-0813        TCGA-14-0862        TCGA-14-0871        TCGA-14-1823 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-15-1446        TCGA-15-1447        TCGA-15-1449        TCGA-16-0846 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-16-1460        TCGA-19-0957        TCGA-19-0962        TCGA-19-1386 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-1389        TCGA-19-1392        TCGA-19-1786        TCGA-19-1789 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-1791        TCGA-19-2619        TCGA-19-2620        TCGA-19-2625 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-2631        TCGA-19-5947        TCGA-19-5950        TCGA-19-5951 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-5952        TCGA-19-5953        TCGA-19-5954        TCGA-19-5955 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-5956        TCGA-19-5958        TCGA-19-5959        TCGA-19-5960 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-26-1440        TCGA-26-1442        TCGA-26-5132        TCGA-26-5133 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-26-5134        TCGA-26-6173        TCGA-26-6174        TCGA-27-1830 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-27-1831        TCGA-27-1832        TCGA-27-1833        TCGA-27-1834 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-27-1836        TCGA-27-2518        TCGA-27-2528        TCGA-28-1746 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-1747        TCGA-28-1750        TCGA-28-1752        TCGA-28-1753 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-1757        TCGA-28-2501        TCGA-28-5208        TCGA-28-5214 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-32-1970        TCGA-32-1976        TCGA-32-1978        TCGA-32-1982 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-32-1986        TCGA-32-1987        TCGA-32-1991        TCGA-32-4210 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-32-4211        TCGA-32-5222        TCGA-41-2573        TCGA-41-2575 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-41-3392        TCGA-41-3393        TCGA-41-3915        TCGA-41-4097 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-41-5651        TCGA-41-6646        TCGA-74-6573        TCGA-74-6575 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-74-6577        TCGA-74-6578        TCGA-74-6581        TCGA-74-6584 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-4926        TCGA-76-4928        TCGA-76-4929        TCGA-76-4931 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-6192        TCGA-76-6193        TCGA-76-6282        TCGA-76-6283 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-6285        TCGA-76-6656        TCGA-76-6657        TCGA-76-6660 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-6662        TCGA-76-6663        TCGA-76-6664        TCGA-81-5910 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
D41V8, multiclass
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                1               200 
       TCGA-02-0003        TCGA-02-0011        TCGA-02-0014        TCGA-02-0068 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-02-0069        TCGA-02-0116        TCGA-02-2470        TCGA-02-2485 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0125        TCGA-06-0126        TCGA-06-0128        TCGA-06-0129 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0130        TCGA-06-0154        TCGA-06-0155        TCGA-06-0171 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0189        TCGA-06-0238        TCGA-06-0644        TCGA-06-0650 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0875        TCGA-06-0876        TCGA-06-0877        TCGA-06-0878 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0879        TCGA-06-0882        TCGA-06-0939        TCGA-06-1084 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-1086        TCGA-06-1087        TCGA-06-1800        TCGA-06-1802 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-1804        TCGA-06-1805        TCGA-06-1806        TCGA-06-2557 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-2558        TCGA-06-2559        TCGA-06-2562        TCGA-06-2563 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-2564        TCGA-06-2565        TCGA-06-2566        TCGA-06-2567 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-2570        TCGA-06-5408        TCGA-06-5410        TCGA-06-5411 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5412        TCGA-06-5413        TCGA-06-5414        TCGA-06-5415 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5416        TCGA-06-5418        TCGA-06-5856        TCGA-06-5858 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5859        TCGA-06-6388        TCGA-06-6389        TCGA-06-6390 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-6391        TCGA-06-6693        TCGA-06-6694        TCGA-06-6695 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-6697        TCGA-06-6698        TCGA-06-6699        TCGA-06-6700 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-6701        TCGA-08-0245        TCGA-08-0344        TCGA-08-0345 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-08-0346        TCGA-08-0347        TCGA-08-0348        TCGA-08-0349 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-08-0350        TCGA-08-0351        TCGA-08-0352        TCGA-08-0353 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-08-0354        TCGA-08-0355        TCGA-08-0356        TCGA-08-0357 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-08-0358        TCGA-08-0359        TCGA-08-0375        TCGA-08-0380 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-08-0386        TCGA-08-0389        TCGA-08-0390        TCGA-08-0392 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-12-0691        TCGA-12-0692        TCGA-12-1598        TCGA-12-1599 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-12-3646        TCGA-12-3649        TCGA-12-3650        TCGA-12-3651 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-12-3652        TCGA-12-3653        TCGA-12-5295        TCGA-12-5301 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-14-0813        TCGA-14-0862        TCGA-14-0871        TCGA-14-1823 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-15-1446        TCGA-15-1447        TCGA-15-1449        TCGA-16-0846 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-16-1460        TCGA-19-0957        TCGA-19-0962        TCGA-19-1386 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-1389        TCGA-19-1392        TCGA-19-1786        TCGA-19-1789 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-1791        TCGA-19-2619        TCGA-19-2620        TCGA-19-2625 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-2631        TCGA-19-5947        TCGA-19-5950        TCGA-19-5951 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-5952        TCGA-19-5953        TCGA-19-5954        TCGA-19-5955 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-5956        TCGA-19-5958        TCGA-19-5959        TCGA-19-5960 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-26-1440        TCGA-26-1442        TCGA-26-5132        TCGA-26-5133 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-26-5134        TCGA-26-6173        TCGA-26-6174        TCGA-27-1830 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-27-1831        TCGA-27-1832        TCGA-27-1833        TCGA-27-1834 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-27-1836        TCGA-27-2518        TCGA-27-2528        TCGA-28-1746 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-1747        TCGA-28-1750        TCGA-28-1752        TCGA-28-1753 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-1757        TCGA-28-2501        TCGA-28-5208        TCGA-28-5214 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-32-1970        TCGA-32-1976        TCGA-32-1978        TCGA-32-1982 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-32-1986        TCGA-32-1987        TCGA-32-1991        TCGA-32-4210 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-32-4211        TCGA-32-5222        TCGA-41-2573        TCGA-41-2575 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-41-3392        TCGA-41-3393        TCGA-41-3915        TCGA-41-4097 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-41-5651        TCGA-41-6646        TCGA-74-6573        TCGA-74-6575 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-74-6577        TCGA-74-6578        TCGA-74-6581        TCGA-74-6584 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-4926        TCGA-76-4928        TCGA-76-4929        TCGA-76-4931 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-6192        TCGA-76-6193        TCGA-76-6282        TCGA-76-6283 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-6285        TCGA-76-6656        TCGA-76-6657        TCGA-76-6660 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-6662        TCGA-76-6663        TCGA-76-6664        TCGA-81-5910 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
D41V9, multiclass
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2               145 
       TCGA-02-0047        TCGA-02-0055        TCGA-02-2483        TCGA-02-2485 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-02-2486        TCGA-06-0125        TCGA-06-0129        TCGA-06-0130 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0132        TCGA-06-0138        TCGA-06-0141        TCGA-06-0157 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0158        TCGA-06-0168        TCGA-06-0174        TCGA-06-0178 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0184        TCGA-06-0187        TCGA-06-0190        TCGA-06-0210 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0211        TCGA-06-0219        TCGA-06-0238        TCGA-06-0644 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0645        TCGA-06-0646        TCGA-06-0649        TCGA-06-0686 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0743        TCGA-06-0744        TCGA-06-0745        TCGA-06-0747 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0749        TCGA-06-0750        TCGA-06-0878        TCGA-06-0882 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-1804        TCGA-06-2557        TCGA-06-2558        TCGA-06-2559 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-2561        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2567        TCGA-06-2569        TCGA-06-2570 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5408        TCGA-06-5410        TCGA-06-5411        TCGA-06-5412 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5413        TCGA-06-5414        TCGA-06-5415        TCGA-06-5416 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5418        TCGA-06-5856        TCGA-06-5858        TCGA-06-5859 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-08-0386        TCGA-12-0616        TCGA-12-0618        TCGA-12-0619 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-12-0821        TCGA-12-3650        TCGA-12-3652        TCGA-12-3653 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-12-5295        TCGA-12-5299        TCGA-14-0781        TCGA-14-0787 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-14-0789        TCGA-14-0790        TCGA-14-0817        TCGA-14-1823 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-14-1825        TCGA-14-1829        TCGA-14-2554        TCGA-15-0742 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-15-1444        TCGA-16-0846        TCGA-16-1045        TCGA-19-1787 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-2619        TCGA-19-2620        TCGA-19-2624        TCGA-19-2625 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-2629        TCGA-19-4065        TCGA-19-5960        TCGA-26-1442 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-26-5132        TCGA-26-5133        TCGA-26-5134        TCGA-26-5135 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-26-5136        TCGA-26-5139        TCGA-27-1830        TCGA-27-1831 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-27-1832        TCGA-27-1834        TCGA-27-1835        TCGA-27-1837 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-27-2519        TCGA-27-2521        TCGA-27-2523        TCGA-27-2524 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-27-2526        TCGA-27-2528        TCGA-28-1747        TCGA-28-1753 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-2509        TCGA-28-2510        TCGA-28-2513        TCGA-28-2514 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-5204        TCGA-28-5207        TCGA-28-5208        TCGA-28-5209 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-5213        TCGA-28-5215        TCGA-28-5216        TCGA-28-5218 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-5220        TCGA-32-1970        TCGA-32-1980        TCGA-32-1982 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-32-2615        TCGA-32-2616        TCGA-32-2632        TCGA-32-2634 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-32-2638        TCGA-32-4213        TCGA-32-5222        TCGA-41-2571 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-41-2572        TCGA-41-3915        TCGA-41-4097        TCGA-41-5651 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-4925        TCGA-76-4926        TCGA-76-4928        TCGA-76-4929 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-4931 
"1Q LOSS WILD-TYPE" 
D41V10, multiclass
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2               145 
       TCGA-02-0047        TCGA-02-0055        TCGA-02-2483        TCGA-02-2485 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-02-2486        TCGA-06-0125        TCGA-06-0129        TCGA-06-0130 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0132        TCGA-06-0138        TCGA-06-0141        TCGA-06-0157 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0158        TCGA-06-0168        TCGA-06-0174        TCGA-06-0178 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0184        TCGA-06-0187        TCGA-06-0190        TCGA-06-0210 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0211        TCGA-06-0219        TCGA-06-0238        TCGA-06-0644 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0645        TCGA-06-0646        TCGA-06-0649        TCGA-06-0686 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0743        TCGA-06-0744        TCGA-06-0745        TCGA-06-0747 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-0749        TCGA-06-0750        TCGA-06-0878        TCGA-06-0882 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-1804        TCGA-06-2557        TCGA-06-2558        TCGA-06-2559 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-2561        TCGA-06-2562        TCGA-06-2563        TCGA-06-2564 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-2565        TCGA-06-2567        TCGA-06-2569        TCGA-06-2570 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5408        TCGA-06-5410        TCGA-06-5411        TCGA-06-5412 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5413        TCGA-06-5414        TCGA-06-5415        TCGA-06-5416 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-06-5418        TCGA-06-5856        TCGA-06-5858        TCGA-06-5859 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-08-0386        TCGA-12-0616        TCGA-12-0618        TCGA-12-0619 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-12-0821        TCGA-12-3650        TCGA-12-3652        TCGA-12-3653 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-12-5295        TCGA-12-5299        TCGA-14-0781        TCGA-14-0787 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-14-0789        TCGA-14-0790        TCGA-14-0817        TCGA-14-1823 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-14-1825        TCGA-14-1829        TCGA-14-2554        TCGA-15-0742 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-15-1444        TCGA-16-0846        TCGA-16-1045        TCGA-19-1787 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-2619        TCGA-19-2620        TCGA-19-2624        TCGA-19-2625 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-19-2629        TCGA-19-4065        TCGA-19-5960        TCGA-26-1442 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-26-5132        TCGA-26-5133        TCGA-26-5134        TCGA-26-5135 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-26-5136        TCGA-26-5139        TCGA-27-1830        TCGA-27-1831 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-27-1832        TCGA-27-1834        TCGA-27-1835        TCGA-27-1837 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-27-2519        TCGA-27-2521        TCGA-27-2523        TCGA-27-2524 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-27-2526        TCGA-27-2528        TCGA-28-1747        TCGA-28-1753 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-2509        TCGA-28-2510        TCGA-28-2513        TCGA-28-2514 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-5204        TCGA-28-5207        TCGA-28-5208        TCGA-28-5209 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-5213        TCGA-28-5215        TCGA-28-5216        TCGA-28-5218 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-28-5220        TCGA-32-1970        TCGA-32-1980        TCGA-32-1982 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-32-2615        TCGA-32-2616        TCGA-32-2632        TCGA-32-2634 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-32-2638        TCGA-32-4213        TCGA-32-5222        TCGA-41-2571 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-41-2572        TCGA-41-3915        TCGA-41-4097        TCGA-41-5651 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-4925        TCGA-76-4926        TCGA-76-4928        TCGA-76-4929 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-76-4931 
"1Q LOSS WILD-TYPE" 

Clustering(42) Variable = 2p loss mutation analysis
D42V1, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0               172
  CLUS_2               6               164
  CLUS_3               4               163
D42V2, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               1               216
  CLUS_2               3               123
  CLUS_3               6               160
D42V3, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               1               138
  CLUS_2               3               154
  CLUS_3               2                70
  CLUS_4               2               102
D42V4, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               1               162
  CLUS_2               2               177
  CLUS_3               5               125
D42V5, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               4               157
  CLUS_2               1               213
  CLUS_3               5               183
D42V6, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0                38
  CLUS_2               1                19
  CLUS_3               0                24
  CLUS_4               2                25
D42V7, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               2                52
  CLUS_2               2                56
  CLUS_3               1                43
  CLUS_4               0                45
D42V8, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               1                63
  CLUS_2               1                32
  CLUS_3               3               101
D42V9, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               3                41
  CLUS_2               0                67
  CLUS_3               0                36
D42V10, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0                66
  CLUS_2               0                21
  CLUS_3               3                57

Clustering(43) Variable = 2q loss mutation analysis
D43V1, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0               172
  CLUS_2               6               164
  CLUS_3               3               164
D43V2, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1               216
  CLUS_2               2               124
  CLUS_3               6               160
D43V3, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0               139
  CLUS_2               3               154
  CLUS_3               2                70
  CLUS_4               2               102
D43V4, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1               162
  CLUS_2               1               178
  CLUS_3               5               125
D43V5, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               3               158
  CLUS_2               1               213
  CLUS_3               5               183
D43V6, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0                38
  CLUS_2               1                19
  CLUS_3               0                24
  CLUS_4               2                25
D43V7, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               2                52
  CLUS_2               2                56
  CLUS_3               1                43
  CLUS_4               0                45
D43V8, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1                63
  CLUS_2               1                32
  CLUS_3               3               101
D43V9, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               3                41
  CLUS_2               0                67
  CLUS_3               0                36
D43V10, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0                66
  CLUS_2               0                21
  CLUS_3               3                57

Clustering(44) Variable = 3p loss mutation analysis
D44V1, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               6               166
  CLUS_2               8               162
  CLUS_3               7               160
D44V2, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              10               207
  CLUS_2               3               123
  CLUS_3               8               158
D44V3, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               5               134
  CLUS_2               5               152
  CLUS_3               5                67
  CLUS_4               5                99
D44V4, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               6               157
  CLUS_2               6               173
  CLUS_3               8               122
D44V5, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              10               151
  CLUS_2               2               212
  CLUS_3              10               178
D44V6, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1                37
  CLUS_2               0                20
  CLUS_3               0                24
  CLUS_4               3                24
D44V7, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               2                52
  CLUS_2               0                58
  CLUS_3               4                40
  CLUS_4               3                42
D44V8, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               4                60
  CLUS_2               1                32
  CLUS_3               4               100
D44V9, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               3                41
  CLUS_2               3                64
  CLUS_3               0                36
D44V10, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               4                62
  CLUS_2               1                20
  CLUS_3               1                59

Clustering(45) Variable = 3q loss mutation analysis
D45V1, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               4               168
  CLUS_2               7               163
  CLUS_3               4               163
D45V2, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               6               211
  CLUS_2               2               124
  CLUS_3               7               159
D45V3, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1               138
  CLUS_2               4               153
  CLUS_3               6                66
  CLUS_4               4               100
D45V4, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               3               160
  CLUS_2               6               173
  CLUS_3               6               124
D45V5, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              10               151
  CLUS_2               0               214
  CLUS_3               6               182
D45V6, multiclass
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2               107 
       TCGA-06-0650        TCGA-06-1804        TCGA-06-1806        TCGA-06-5408 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-6388        TCGA-06-6389 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-06-6390        TCGA-06-6391        TCGA-06-6693        TCGA-06-6694 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-06-6695        TCGA-06-6697        TCGA-06-6698        TCGA-06-6699 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-06-6700        TCGA-06-6701        TCGA-12-5295        TCGA-12-5299 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-12-5301        TCGA-14-0740        TCGA-14-0781        TCGA-14-0862 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-14-1043        TCGA-14-1395        TCGA-14-1450        TCGA-15-1444 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-19-4065        TCGA-19-5947        TCGA-19-5950        TCGA-19-5951 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-19-5952        TCGA-19-5953        TCGA-19-5954        TCGA-19-5955 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-19-5956        TCGA-19-5958        TCGA-19-5959        TCGA-19-5960 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-26-6173 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-26-6174        TCGA-28-2501        TCGA-28-2510        TCGA-28-5204 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-28-5207        TCGA-28-5208        TCGA-28-5209        TCGA-28-5211 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-28-5213        TCGA-28-5214        TCGA-28-5215        TCGA-28-5216 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5219        TCGA-28-5220        TCGA-28-6450 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-32-1979        TCGA-32-1980        TCGA-32-5222        TCGA-41-5651 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4925 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-76-4926        TCGA-76-4928        TCGA-76-4931        TCGA-76-4934 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-76-4935        TCGA-76-6191        TCGA-76-6192        TCGA-76-6193 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-76-6280        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-76-6286        TCGA-76-6656        TCGA-76-6657        TCGA-76-6660 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-76-6661        TCGA-76-6662        TCGA-76-6663        TCGA-76-6664 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-81-5910        TCGA-81-5911        TCGA-87-5896 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
D45V7, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               2                52
  CLUS_2               1                57
  CLUS_3               2                42
  CLUS_4               2                43
D45V8, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               2                62
  CLUS_2               1                32
  CLUS_3               4               100
D45V9, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               2                42
  CLUS_2               1                66
  CLUS_3               0                36
D45V10, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               2                64
  CLUS_2               1                20
  CLUS_3               0                60

Clustering(46) Variable = 4p loss mutation analysis
D46V1, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               3               169
  CLUS_2              14               156
  CLUS_3               7               160
D46V2, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               9               208
  CLUS_2               5               121
  CLUS_3              10               156
D46V3, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               3               136
  CLUS_2              12               145
  CLUS_3               4                68
  CLUS_4               5                99
D46V4, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               5               158
  CLUS_2               6               173
  CLUS_3              13               117
D46V5, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               7               154
  CLUS_2               9               205
  CLUS_3              10               178
D46V6, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               2                36
  CLUS_2               1                19
  CLUS_3               1                23
  CLUS_4               0                27
D46V7, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               1                53
  CLUS_2               2                56
  CLUS_3               6                38
  CLUS_4               3                42
D46V8, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               6                58
  CLUS_2               1                32
  CLUS_3               5                99
D46V9, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               0                44
  CLUS_2               3                64
  CLUS_3               3                33
D46V10, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               4                62
  CLUS_2               1                20
  CLUS_3               1                59

Clustering(47) Variable = 4q loss mutation analysis
D47V1, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               4               168
  CLUS_2              13               157
  CLUS_3               5               162
D47V2, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               9               208
  CLUS_2               4               122
  CLUS_3               9               157
D47V3, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               2               137
  CLUS_2              10               147
  CLUS_3               4                68
  CLUS_4               5                99
D47V4, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               5               158
  CLUS_2               6               173
  CLUS_3              10               120
D47V5, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              11               150
  CLUS_2               5               209
  CLUS_3               9               179
D47V6, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               1                37
  CLUS_2               0                20
  CLUS_3               1                23
  CLUS_4               2                25
D47V7, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               1                53
  CLUS_2               1                57
  CLUS_3               5                39
  CLUS_4               3                42
D47V8, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               5                59
  CLUS_2               1                32
  CLUS_3               4               100
D47V9, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               2                42
  CLUS_2               1                66
  CLUS_3               2                34
D47V10, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               3                63
  CLUS_2               1                20
  CLUS_3               1                59

Clustering(48) Variable = 5p loss mutation analysis
D48V1, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               1               171
  CLUS_2              12               158
  CLUS_3               7               160
D48V2, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               4               213
  CLUS_2               7               119
  CLUS_3               9               157
D48V3, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               3               136
  CLUS_2              11               146
  CLUS_3               2                70
  CLUS_4               3               101
D48V4, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               3               160
  CLUS_2               7               172
  CLUS_3               9               121
D48V5, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               6               155
  CLUS_2               4               210
  CLUS_3              11               177
D48V6, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               0                38
  CLUS_2               0                20
  CLUS_3               1                23
  CLUS_4               3                24
D48V7, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               4                50
  CLUS_2               1                57
  CLUS_3               3                41
  CLUS_4               2                43
D48V8, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               3                61
  CLUS_2               1                32
  CLUS_3               6                98
D48V9, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               3                41
  CLUS_2               3                64
  CLUS_3               1                35
D48V10, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               3                63
  CLUS_2               2                19
  CLUS_3               2                58

Clustering(49) Variable = 5q loss mutation analysis
D49V1, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               3               169
  CLUS_2              11               159
  CLUS_3               5               162
D49V2, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               7               210
  CLUS_2               5               121
  CLUS_3               7               159
D49V3, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               3               136
  CLUS_2              10               147
  CLUS_3               2                70
  CLUS_4               3               101
D49V4, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               4               159
  CLUS_2               5               174
  CLUS_3               9               121
D49V5, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               6               155
  CLUS_2               3               211
  CLUS_3              11               177
D49V6, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                38
  CLUS_2               0                20
  CLUS_3               1                23
  CLUS_4               3                24
D49V7, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               3                51
  CLUS_2               2                56
  CLUS_3               3                41
  CLUS_4               2                43
D49V8, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               3                61
  CLUS_2               1                32
  CLUS_3               6                98
D49V9, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               4                40
  CLUS_2               3                64
  CLUS_3               1                35
D49V10, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               4                62
  CLUS_2               2                19
  CLUS_3               2                58

Clustering(50) Variable = 6p loss mutation analysis
D50V1, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              15               157
  CLUS_2              14               156
  CLUS_3              15               152
D50V2, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              17               200
  CLUS_2              14               112
  CLUS_3              13               153
D50V3, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              14               125
  CLUS_2              17               140
  CLUS_3               4                68
  CLUS_4               6                98
D50V4, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              11               152
  CLUS_2              18               161
  CLUS_3              12               118
D50V5, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              33               128
  CLUS_2               6               208
  CLUS_3               8               180
D50V6, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2                36
  CLUS_2               3                17
  CLUS_3               2                22
  CLUS_4               2                25
D50V7, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               6                48
  CLUS_2               5                53
  CLUS_3               3                41
  CLUS_4               4                41
D50V8, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               4                60
  CLUS_2               4                29
  CLUS_3              10                94
D50V9, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               5                39
  CLUS_2               7                60
  CLUS_3               5                31
D50V10, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               6                60
  CLUS_2               2                19
  CLUS_3               9                51

Clustering(51) Variable = 6q loss mutation analysis
D51V1, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              24               148
  CLUS_2              23               147
  CLUS_3              28               139
D51V2, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              31               186
  CLUS_2              22               104
  CLUS_3              22               144
D51V3, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              25               114
  CLUS_2              23               134
  CLUS_3               8                64
  CLUS_4              12                92
D51V4, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              17               146
  CLUS_2              33               146
  CLUS_3              18               112
D51V5, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              46               115
  CLUS_2              21               193
  CLUS_3              13               175
D51V6, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               3                35
  CLUS_2               6                14
  CLUS_3               6                18
  CLUS_4               3                24
D51V7, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               8                46
  CLUS_2               6                52
  CLUS_3               6                38
  CLUS_4               5                40
D51V8, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               9                55
  CLUS_2               5                28
  CLUS_3              11                93
D51V9, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               7                37
  CLUS_2              14                53
  CLUS_3               6                30
D51V10, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              12                54
  CLUS_2               6                15
  CLUS_3               9                51

Clustering(52) Variable = 7p loss mutation analysis
D52V1, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               1               171
  CLUS_2               3               167
  CLUS_3               1               166
D52V2, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               1               216
  CLUS_2               1               125
  CLUS_3               3               163
D52V3, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               1               138
  CLUS_2               3               154
  CLUS_3               0                72
  CLUS_4               1               103
D52V4, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0               163
  CLUS_2               1               178
  CLUS_3               4               126
D52V5, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               1               160
  CLUS_2               1               213
  CLUS_3               3               185
D52V6, multiclass
D52V7, multiclass
D52V8, multiclass
D52V9, multiclass
D52V10, multiclass

Clustering(53) Variable = 7q loss mutation analysis
D53V1, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               1               171
  CLUS_2               2               168
  CLUS_3               1               166
D53V2, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               1               216
  CLUS_2               1               125
  CLUS_3               2               164
D53V3, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               1               138
  CLUS_2               2               155
  CLUS_3               0                72
  CLUS_4               1               103
D53V4, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               0               163
  CLUS_2               1               178
  CLUS_3               3               127
D53V5, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               1               160
  CLUS_2               1               213
  CLUS_3               2               186
D53V6, multiclass
D53V7, multiclass
D53V8, multiclass
D53V9, multiclass
D53V10, multiclass

Clustering(54) Variable = 8p loss mutation analysis
D54V1, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              11               161
  CLUS_2               9               161
  CLUS_3              11               156
D54V2, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              16               201
  CLUS_2               7               119
  CLUS_3               8               158
D54V3, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              11               128
  CLUS_2              10               147
  CLUS_3               3                69
  CLUS_4               6                98
D54V4, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               8               155
  CLUS_2              16               163
  CLUS_3               6               124
D54V5, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              14               147
  CLUS_2              11               203
  CLUS_3               9               179
D54V6, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               2                36
  CLUS_2               0                20
  CLUS_3               3                21
  CLUS_4               0                27
D54V7, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               4                50
  CLUS_2               2                56
  CLUS_3               1                43
  CLUS_4               3                42
D54V8, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               3                61
  CLUS_2               2                31
  CLUS_3               5                99
D54V9, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               2                42
  CLUS_2               5                62
  CLUS_3               1                35
D54V10, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               5                61
  CLUS_2               1                20
  CLUS_3               2                58

Clustering(55) Variable = 8q loss mutation analysis
D55V1, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               8               164
  CLUS_2               5               165
  CLUS_3               7               160
D55V2, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              13               204
  CLUS_2               3               123
  CLUS_3               4               162
D55V3, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               9               130
  CLUS_2               4               153
  CLUS_3               2                70
  CLUS_4               4               100
D55V4, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               7               156
  CLUS_2              10               169
  CLUS_3               2               128
D55V5, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              12               149
  CLUS_2               6               208
  CLUS_3               3               185
D55V6, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2               107 
       TCGA-06-0650        TCGA-06-1804        TCGA-06-1806        TCGA-06-5410 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-06-5411        TCGA-06-5412        TCGA-06-5413        TCGA-06-5414 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-06-5415        TCGA-06-5416        TCGA-06-5418        TCGA-06-5856 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-06-5858        TCGA-06-5859        TCGA-06-6388        TCGA-06-6389 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-06-6390        TCGA-06-6391        TCGA-06-6693        TCGA-06-6694 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-06-6695        TCGA-06-6697        TCGA-06-6698        TCGA-06-6699 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-06-6700        TCGA-06-6701        TCGA-12-5295        TCGA-12-5299 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-12-5301        TCGA-14-0740        TCGA-14-0781        TCGA-14-0862 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-14-1043        TCGA-14-1395        TCGA-15-1444        TCGA-19-4065 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-19-5947        TCGA-19-5950        TCGA-19-5951        TCGA-19-5952 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-19-5953        TCGA-19-5954        TCGA-19-5955        TCGA-19-5956 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-19-5958        TCGA-19-5959        TCGA-19-5960        TCGA-26-1442 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-26-5132        TCGA-26-5133        TCGA-26-5134        TCGA-26-5135 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-26-5136        TCGA-26-5139        TCGA-26-6173        TCGA-26-6174 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-28-2501        TCGA-28-2510        TCGA-28-5204        TCGA-28-5207 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-28-5208        TCGA-28-5209        TCGA-28-5211        TCGA-28-5213 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-28-5214        TCGA-28-5215        TCGA-28-5216        TCGA-28-5218 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-28-5219        TCGA-28-5220        TCGA-28-6450        TCGA-32-1979 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-32-1980        TCGA-32-5222        TCGA-41-5651        TCGA-41-6646 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-74-6573        TCGA-74-6575        TCGA-74-6577        TCGA-74-6578 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-74-6581        TCGA-74-6584        TCGA-76-4925        TCGA-76-4926 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-4934 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-76-4935        TCGA-76-6191        TCGA-76-6192        TCGA-76-6193 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-76-6280        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-76-6286        TCGA-76-6656        TCGA-76-6657        TCGA-76-6660 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-76-6661        TCGA-76-6662        TCGA-76-6663        TCGA-76-6664 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-81-5910        TCGA-81-5911        TCGA-87-5896 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D55V7, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               2                52
  CLUS_2               0                58
  CLUS_3               0                44
  CLUS_4               2                43
D55V8, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               1                63
  CLUS_2               1                32
  CLUS_3               2               102
D55V9, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               1                43
  CLUS_2               3                64
  CLUS_3               1                35
D55V10, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               4                62
  CLUS_2               0                21
  CLUS_3               1                59

Clustering(56) Variable = 9p loss mutation analysis
D56V1, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              47               125
  CLUS_2              40               130
  CLUS_3              63               104
D56V2, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              59               158
  CLUS_2              53                73
  CLUS_3              38               128
D56V3, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              42                97
  CLUS_2              43               114
  CLUS_3              21                51
  CLUS_4              34                70
D56V4, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              46               117
  CLUS_2              62               117
  CLUS_3              32                98
D56V5, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              45               116
  CLUS_2              71               143
  CLUS_3              48               140
D56V6, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              11                27
  CLUS_2               6                14
  CLUS_3               7                17
  CLUS_4               6                21
D56V7, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              20                34
  CLUS_2              13                45
  CLUS_3              16                28
  CLUS_4              16                29
D56V8, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              27                37
  CLUS_2              12                21
  CLUS_3              26                78
D56V9, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               7                37
  CLUS_2              20                47
  CLUS_3              15                21
D56V10, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              14                52
  CLUS_2              11                10
  CLUS_3              17                43

Clustering(57) Variable = 9q loss mutation analysis
D57V1, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              20               152
  CLUS_2              12               158
  CLUS_3              26               141
D57V2, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              21               196
  CLUS_2              23               103
  CLUS_3              14               152
D57V3, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              16               123
  CLUS_2              20               137
  CLUS_3               5                67
  CLUS_4              14                90
D57V4, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              18               145
  CLUS_2              26               153
  CLUS_3              11               119
D57V5, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              25               136
  CLUS_2              24               190
  CLUS_3              14               174
D57V6, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               2                36
  CLUS_2               1                19
  CLUS_3               2                22
  CLUS_4               4                23
D57V7, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               7                47
  CLUS_2               1                57
  CLUS_3               7                37
  CLUS_4               6                39
D57V8, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              11                53
  CLUS_2               4                29
  CLUS_3               6                98
D57V9, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               4                40
  CLUS_2              10                57
  CLUS_3               3                33
D57V10, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               7                59
  CLUS_2               5                16
  CLUS_3               5                55

Clustering(58) Variable = 10p loss mutation analysis
D58V1, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1              131                 41
  CLUS_2              112                 58
  CLUS_3              149                 18
D58V2, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1              169                 48
  CLUS_2              113                 13
  CLUS_3              110                 56
D58V3, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1              120                 19
  CLUS_2              118                 39
  CLUS_3               52                 20
  CLUS_4               79                 25
D58V4, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1              136                 27
  CLUS_2              156                 23
  CLUS_3               77                 53
D58V5, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1              137                 24
  CLUS_2              205                  9
  CLUS_3               95                 93
D58V6, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               27                 11
  CLUS_2               20                  0
  CLUS_3               23                  1
  CLUS_4               20                  7
D58V7, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               43                 11
  CLUS_2               39                 19
  CLUS_3               43                  1
  CLUS_4               38                  7
D58V8, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               61                  3
  CLUS_2               25                  8
  CLUS_3               77                 27
D58V9, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               35                  9
  CLUS_2               56                 11
  CLUS_3               32                  4
D58V10, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               54                 12
  CLUS_2               21                  0
  CLUS_3               48                 12

Clustering(59) Variable = 10q loss mutation analysis
D59V1, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1              133                 39
  CLUS_2              120                 50
  CLUS_3              153                 14
D59V2, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1              172                 45
  CLUS_2              117                  9
  CLUS_3              117                 49
D59V3, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1              123                 16
  CLUS_2              126                 31
  CLUS_3               52                 20
  CLUS_4               82                 22
D59V4, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1              137                 26
  CLUS_2              159                 20
  CLUS_3               87                 43
D59V5, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1              140                 21
  CLUS_2              210                  4
  CLUS_3              100                 88
D59V6, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               27                 11
  CLUS_2               20                  0
  CLUS_3               23                  1
  CLUS_4               19                  8
D59V7, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               42                 12
  CLUS_2               40                 18
  CLUS_3               44                  0
  CLUS_4               39                  6
D59V8, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               61                  3
  CLUS_2               25                  8
  CLUS_3               79                 25
D59V9, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               36                  8
  CLUS_2               57                 10
  CLUS_3               32                  4
D59V10, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               55                 11
  CLUS_2               21                  0
  CLUS_3               49                 11

Clustering(60) Variable = 11p loss mutation analysis
D60V1, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               18                154
  CLUS_2               38                132
  CLUS_3                5                162
D60V2, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               22                195
  CLUS_2                4                122
  CLUS_3               35                131
D60V3, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               10                129
  CLUS_2               26                131
  CLUS_3               10                 62
  CLUS_4               13                 91
D60V4, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               18                145
  CLUS_2                9                170
  CLUS_3               32                 98
D60V5, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               38                123
  CLUS_2                3                211
  CLUS_3               23                165
D60V6, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                0                 38
  CLUS_2                1                 19
  CLUS_3                0                 24
  CLUS_4                6                 21
D60V7, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                8                 46
  CLUS_2                7                 51
  CLUS_3                3                 41
  CLUS_4                5                 40
D60V8, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                3                 61
  CLUS_2                3                 30
  CLUS_3               17                 87
D60V9, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               10                 34
  CLUS_2                6                 61
  CLUS_3                2                 34
D60V10, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                6                 60
  CLUS_2                2                 19
  CLUS_3               10                 50

Clustering(61) Variable = 11q loss mutation analysis
D61V1, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               18                154
  CLUS_2               30                140
  CLUS_3                6                161
D61V2, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               23                194
  CLUS_2                5                121
  CLUS_3               26                140
D61V3, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               11                128
  CLUS_2               19                138
  CLUS_3               10                 62
  CLUS_4               11                 93
D61V4, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               19                144
  CLUS_2               10                169
  CLUS_3               22                108
D61V5, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               36                125
  CLUS_2                4                210
  CLUS_3               15                173
D61V6, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                0                 38
  CLUS_2                1                 19
  CLUS_3                1                 23
  CLUS_4                2                 25
D61V7, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                6                 48
  CLUS_2                4                 54
  CLUS_3                2                 42
  CLUS_4                5                 40
D61V8, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                2                 31
  CLUS_3               13                 91
D61V9, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                5                 39
  CLUS_2                8                 59
  CLUS_3                2                 34
D61V10, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                8                 58
  CLUS_2                2                 19
  CLUS_3                5                 55

Clustering(62) Variable = 12p loss mutation analysis
D62V1, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               10                162
  CLUS_2               20                150
  CLUS_3                6                161
D62V2, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               13                204
  CLUS_2                4                122
  CLUS_3               19                147
D62V3, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               11                128
  CLUS_2               16                141
  CLUS_3                6                 66
  CLUS_4                3                101
D62V4, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                6                157
  CLUS_2               15                164
  CLUS_3               15                115
D62V5, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               13                148
  CLUS_2               13                201
  CLUS_3               12                176
D62V6, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                2                 36
  CLUS_2                2                 18
  CLUS_3                1                 23
  CLUS_4                0                 27
D62V7, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                1                 53
  CLUS_2                4                 54
  CLUS_3                4                 40
  CLUS_4                0                 45
D62V8, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                4                 60
  CLUS_2                0                 33
  CLUS_3                5                 99
D62V9, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                3                 41
  CLUS_2                5                 62
  CLUS_3                2                 34
D62V10, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                5                 61
  CLUS_2                1                 20
  CLUS_3                4                 56

Clustering(63) Variable = 12q loss mutation analysis
D63V1, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                6                166
  CLUS_2               19                151
  CLUS_3                7                160
D63V2, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                9                208
  CLUS_2                5                121
  CLUS_3               18                148
D63V3, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                8                131
  CLUS_2               14                143
  CLUS_3                4                 68
  CLUS_4                5                 99
D63V4, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                6                157
  CLUS_2               11                168
  CLUS_3               14                116
D63V5, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               15                146
  CLUS_2                9                205
  CLUS_3               11                177
D63V6, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                1                 37
  CLUS_2                3                 17
  CLUS_3                0                 24
  CLUS_4                2                 25
D63V7, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                2                 52
  CLUS_2                4                 54
  CLUS_3                5                 39
  CLUS_4                0                 45
D63V8, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                5                 59
  CLUS_2                1                 32
  CLUS_3                5                 99
D63V9, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                4                 40
  CLUS_2                4                 63
  CLUS_3                2                 34
D63V10, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                5                 61
  CLUS_2                0                 21
  CLUS_3                5                 55

Clustering(64) Variable = 13q loss mutation analysis
D64V1, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               51                121
  CLUS_2               49                121
  CLUS_3               24                143
D64V2, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               63                154
  CLUS_2               13                113
  CLUS_3               48                118
D64V3, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               36                103
  CLUS_2               38                119
  CLUS_3               23                 49
  CLUS_4               24                 80
D64V4, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               39                124
  CLUS_2               45                134
  CLUS_3               37                 93
D64V5, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               68                 93
  CLUS_2               20                194
  CLUS_3               50                138
D64V6, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                6                 32
  CLUS_2                3                 17
  CLUS_3                2                 22
  CLUS_4               14                 13
D64V7, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               14                 40
  CLUS_2               13                 45
  CLUS_3                7                 37
  CLUS_4               12                 33
D64V8, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                8                 56
  CLUS_2                6                 27
  CLUS_3               32                 72
D64V9, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               14                 30
  CLUS_2               12                 55
  CLUS_3                7                 29
D64V10, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               17                 49
  CLUS_2                2                 19
  CLUS_3               14                 46

Clustering(65) Variable = 14q loss mutation analysis
D65V1, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               47                125
  CLUS_2               52                118
  CLUS_3               15                152
D65V2, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               51                166
  CLUS_2               18                108
  CLUS_3               45                121
D65V3, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               27                112
  CLUS_2               40                117
  CLUS_3               17                 55
  CLUS_4               21                 83
D65V4, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               36                127
  CLUS_2               43                136
  CLUS_3               26                104
D65V5, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               85                 76
  CLUS_2                4                210
  CLUS_3               32                156
D65V6, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                8                 30
  CLUS_2                5                 15
  CLUS_3                1                 23
  CLUS_4               11                 16
D65V7, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               13                 41
  CLUS_2               14                 44
  CLUS_3                7                 37
  CLUS_4               10                 35
D65V8, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                8                 56
  CLUS_2                7                 26
  CLUS_3               29                 75
D65V9, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               19                 25
  CLUS_2               14                 53
  CLUS_3                9                 27
D65V10, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               17                 49
  CLUS_2                1                 20
  CLUS_3               24                 36

Clustering(66) Variable = 15q loss mutation analysis
D66V1, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               17                155
  CLUS_2               34                136
  CLUS_3                8                159
D66V2, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               23                194
  CLUS_2                5                121
  CLUS_3               31                135
D66V3, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                8                131
  CLUS_2               28                129
  CLUS_3               13                 59
  CLUS_4                6                 98
D66V4, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                6                157
  CLUS_2               20                159
  CLUS_3               29                101
D66V5, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               35                126
  CLUS_2               13                201
  CLUS_3               14                174
D66V6, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                 37
  CLUS_2                2                 18
  CLUS_3                0                 24
  CLUS_4                9                 18
D66V7, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                8                 46
  CLUS_2               13                 45
  CLUS_3                3                 41
  CLUS_4                4                 41
D66V8, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                3                 61
  CLUS_2                5                 28
  CLUS_3               20                 84
D66V9, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               12                 32
  CLUS_2                7                 60
  CLUS_3                2                 34
D66V10, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               11                 55
  CLUS_2                1                 20
  CLUS_3                9                 51

Clustering(67) Variable = 16p loss mutation analysis
D67V1, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                8                164
  CLUS_2               11                159
  CLUS_3                4                163
D67V2, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               10                207
  CLUS_2                4                122
  CLUS_3                9                157
D67V3, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                6                133
  CLUS_2                6                151
  CLUS_3                2                 70
  CLUS_4                8                 96
D67V4, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                9                154
  CLUS_2                7                172
  CLUS_3                6                124
D67V5, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               11                150
  CLUS_2                7                207
  CLUS_3                5                183
D67V6, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                 38
  CLUS_2                1                 19
  CLUS_3                1                 23
  CLUS_4                1                 26
D67V7, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                2                 52
  CLUS_2                1                 57
  CLUS_3                2                 42
  CLUS_4                3                 42
D67V8, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                1                 32
  CLUS_3                5                 99
D67V9, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                2                 42
  CLUS_2                6                 61
  CLUS_3                1                 35
D67V10, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                4                 62
  CLUS_2                3                 18
  CLUS_3                2                 58

Clustering(68) Variable = 16q loss mutation analysis
D68V1, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               14                158
  CLUS_2               17                153
  CLUS_3                7                160
D68V2, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               22                195
  CLUS_2                3                123
  CLUS_3               13                153
D68V3, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               14                125
  CLUS_2                8                149
  CLUS_3                3                 69
  CLUS_4               12                 92
D68V4, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               16                147
  CLUS_2               12                167
  CLUS_3                9                121
D68V5, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               16                145
  CLUS_2               12                202
  CLUS_3               13                175
D68V6, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                1                 37
  CLUS_2                1                 19
  CLUS_3                4                 20
  CLUS_4                2                 25
D68V7, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                7                 47
  CLUS_2                1                 57
  CLUS_3                4                 40
  CLUS_4                6                 39
D68V8, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                5                 59
  CLUS_2                3                 30
  CLUS_3               10                 94
D68V9, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                4                 40
  CLUS_2                7                 60
  CLUS_3                2                 34
D68V10, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                6                 60
  CLUS_2                3                 18
  CLUS_3                4                 56

Clustering(69) Variable = 17p loss mutation analysis
D69V1, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               10                162
  CLUS_2               14                156
  CLUS_3                8                159
D69V2, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               12                205
  CLUS_2                7                119
  CLUS_3               13                153
D69V3, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               10                129
  CLUS_2               12                145
  CLUS_3                4                 68
  CLUS_4                5                 99
D69V4, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               10                153
  CLUS_2               10                169
  CLUS_3               11                119
D69V5, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               20                141
  CLUS_2                2                212
  CLUS_3               14                174
D69V6, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                 36
  CLUS_2                2                 18
  CLUS_3                0                 24
  CLUS_4                4                 23
D69V7, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                7                 47
  CLUS_2                6                 52
  CLUS_3                3                 41
  CLUS_4                0                 45
D69V8, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                 60
  CLUS_2                3                 30
  CLUS_3                9                 95
D69V9, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                 42
  CLUS_2                6                 61
  CLUS_3                4                 32
D69V10, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                6                 60
  CLUS_2                1                 20
  CLUS_3                5                 55

Clustering(70) Variable = 17q loss mutation analysis
D70V1, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                7                165
  CLUS_2                3                167
  CLUS_3                7                160
D70V2, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                9                208
  CLUS_2                6                120
  CLUS_3                2                164
D70V3, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                8                131
  CLUS_2                4                153
  CLUS_3                1                 71
  CLUS_4                4                100
D70V4, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                7                156
  CLUS_2                8                171
  CLUS_3                2                128
D70V5, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               11                150
  CLUS_2                1                213
  CLUS_3                7                181
D70V6, multiclass
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                107 
        TCGA-06-0650         TCGA-06-1804         TCGA-06-1806 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5299         TCGA-12-5301 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-14-0740         TCGA-14-0781         TCGA-14-0862 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-14-1043         TCGA-14-1395         TCGA-14-1450 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-15-1444         TCGA-19-5947         TCGA-19-5950 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-19-5951         TCGA-19-5952         TCGA-19-5953 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-19-5954         TCGA-19-5955         TCGA-19-5956 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-19-5958         TCGA-19-5959         TCGA-19-5960 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-26-1442         TCGA-26-5132         TCGA-26-5133 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-26-5134         TCGA-26-5135         TCGA-26-5136 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-26-5139         TCGA-26-6173         TCGA-26-6174 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-28-2501         TCGA-28-2510         TCGA-28-5204 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-28-5211         TCGA-28-5213         TCGA-28-5214 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-28-5215         TCGA-28-5216         TCGA-28-5218 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-28-5219         TCGA-28-5220         TCGA-28-6450 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-32-1979         TCGA-32-1980         TCGA-32-5222 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-41-5651         TCGA-41-6646         TCGA-74-6573 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-74-6575         TCGA-74-6577         TCGA-74-6578 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-74-6581         TCGA-74-6584         TCGA-76-4925 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-76-4931         TCGA-76-4934         TCGA-76-4935 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-76-6191         TCGA-76-6192         TCGA-76-6193 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-76-6280         TCGA-76-6282         TCGA-76-6283 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-76-6286         TCGA-76-6656         TCGA-76-6657 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-76-6660         TCGA-76-6661         TCGA-76-6662 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-76-6663         TCGA-76-6664         TCGA-81-5910 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-81-5911         TCGA-87-5896 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
D70V7, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                3                 51
  CLUS_2                1                 57
  CLUS_3                3                 41
  CLUS_4                0                 45
D70V8, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                4                 60
  CLUS_2                1                 32
  CLUS_3                2                102
D70V9, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                 44
  CLUS_2                5                 62
  CLUS_3                1                 35
D70V10, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                5                 61
  CLUS_2                1                 20
  CLUS_3                0                 60

Clustering(71) Variable = 18p loss mutation analysis
D71V1, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               16                156
  CLUS_2               16                154
  CLUS_3                5                162
D71V2, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               17                200
  CLUS_2                4                122
  CLUS_3               16                150
D71V3, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                8                131
  CLUS_2               14                143
  CLUS_3                3                 69
  CLUS_4                9                 95
D71V4, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               12                151
  CLUS_2               11                168
  CLUS_3               11                119
D71V5, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               21                140
  CLUS_2                7                207
  CLUS_3               16                172
D71V6, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                 35
  CLUS_2                4                 16
  CLUS_3                1                 23
  CLUS_4                7                 20
D71V7, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                5                 49
  CLUS_2                7                 51
  CLUS_3                1                 43
  CLUS_4                6                 39
D71V8, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                2                 31
  CLUS_3               15                 89
D71V9, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                7                 37
  CLUS_2                3                 64
  CLUS_3                1                 35
D71V10, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                6                 60
  CLUS_2                0                 21
  CLUS_3                5                 55

Clustering(72) Variable = 18q loss mutation analysis
D72V1, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               13                159
  CLUS_2               14                156
  CLUS_3                7                160
D72V2, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               16                201
  CLUS_2                5                121
  CLUS_3               13                153
D72V3, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               13                126
  CLUS_2               10                147
  CLUS_3                2                 70
  CLUS_4                8                 96
D72V4, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               12                151
  CLUS_2               13                166
  CLUS_3                8                122
D72V5, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               16                145
  CLUS_2                9                205
  CLUS_3               14                174
D72V6, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                2                 36
  CLUS_2                3                 17
  CLUS_3                0                 24
  CLUS_4                5                 22
D72V7, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                3                 51
  CLUS_2                8                 50
  CLUS_3                1                 43
  CLUS_4                5                 40
D72V8, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                 63
  CLUS_2                1                 32
  CLUS_3               15                 89
D72V9, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                5                 39
  CLUS_2                4                 63
  CLUS_3                2                 34
D72V10, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                4                 62
  CLUS_2                1                 20
  CLUS_3                6                 54

Clustering(73) Variable = 19p loss mutation analysis
D73V1, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                3                169
  CLUS_2                9                161
  CLUS_3                0                167
D73V2, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                4                213
  CLUS_2                0                126
  CLUS_3                8                158
D73V3, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                1                138
  CLUS_2               11                146
  CLUS_3                0                 72
  CLUS_4                0                104
D73V4, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                0                163
  CLUS_2                5                174
  CLUS_3                7                123
D73V5, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                7                154
  CLUS_2                3                211
  CLUS_3                3                185
D73V6, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                1                 37
  CLUS_2                1                 19
  CLUS_3                0                 24
  CLUS_4                2                 25
D73V7, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                0                 54
  CLUS_2                3                 55
  CLUS_3                1                 43
  CLUS_4                1                 44
D73V8, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                1                 63
  CLUS_2                0                 33
  CLUS_3                4                100
D73V9, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                2                 42
  CLUS_2                2                 65
  CLUS_3                0                 36
D73V10, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                4                 62
  CLUS_2                0                 21
  CLUS_3                0                 60

Clustering(74) Variable = 19q loss mutation analysis
D74V1, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                5                167
  CLUS_2               11                159
  CLUS_3                1                166
D74V2, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                6                211
  CLUS_2                1                125
  CLUS_3               10                156
D74V3, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                2                137
  CLUS_2               12                145
  CLUS_3                0                 72
  CLUS_4                3                101
D74V4, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                162
  CLUS_2                5                174
  CLUS_3               11                119
D74V5, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                9                152
  CLUS_2                3                211
  CLUS_3                6                182
D74V6, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                 37
  CLUS_2                1                 19
  CLUS_3                0                 24
  CLUS_4                2                 25
D74V7, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                0                 54
  CLUS_2                3                 55
  CLUS_3                1                 43
  CLUS_4                1                 44
D74V8, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                 63
  CLUS_2                0                 33
  CLUS_3                4                100
D74V9, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                2                 42
  CLUS_2                2                 65
  CLUS_3                1                 35
D74V10, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                4                 62
  CLUS_2                0                 21
  CLUS_3                1                 59

Clustering(75) Variable = 20p loss mutation analysis
D75V1, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                5                167
  CLUS_2                5                165
  CLUS_3                0                167
D75V2, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                5                212
  CLUS_2                0                126
  CLUS_3                5                161
D75V3, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                1                138
  CLUS_2                4                153
  CLUS_3                4                 68
  CLUS_4                1                103
D75V4, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                1                162
  CLUS_2                3                176
  CLUS_3                6                124
D75V5, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                7                154
  CLUS_2                0                214
  CLUS_3                4                184
D75V6, multiclass
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                108 
        TCGA-06-0650         TCGA-06-1804         TCGA-06-1806 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5299         TCGA-12-5301 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-14-0740         TCGA-14-0781         TCGA-14-0862 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-14-1043         TCGA-14-1395         TCGA-14-1450 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-15-1444         TCGA-19-4065         TCGA-19-5947 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-19-5950         TCGA-19-5951         TCGA-19-5952 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-19-5953         TCGA-19-5954         TCGA-19-5955 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-19-5956         TCGA-19-5958         TCGA-19-5959 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-26-5136         TCGA-26-5139         TCGA-26-6173 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-26-6174         TCGA-28-2501         TCGA-28-2510 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5211         TCGA-28-5213 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-5214         TCGA-28-5215         TCGA-28-5216 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-5218         TCGA-28-5219         TCGA-28-5220 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-6450         TCGA-32-1979         TCGA-32-1980 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-32-5222         TCGA-41-5651         TCGA-41-6646 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-74-6573         TCGA-74-6575         TCGA-74-6577 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-74-6578         TCGA-74-6581         TCGA-74-6584 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-76-4925         TCGA-76-4926         TCGA-76-4928 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931         TCGA-76-4934 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-76-4935         TCGA-76-6191         TCGA-76-6192 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-76-6193         TCGA-76-6280         TCGA-76-6282 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-76-6283         TCGA-76-6285         TCGA-76-6656 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-76-6657         TCGA-76-6660         TCGA-76-6661 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-76-6662         TCGA-76-6663         TCGA-76-6664 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-81-5910         TCGA-81-5911         TCGA-87-5896 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
D75V7, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                 52
  CLUS_2                2                 56
  CLUS_3                0                 44
  CLUS_4                0                 45
D75V8, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                0                 64
  CLUS_2                1                 32
  CLUS_3                3                101
D75V9, multiclass
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2569         TCGA-06-2570 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-08-0386         TCGA-12-0616         TCGA-12-0618 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-12-0619         TCGA-12-0821         TCGA-12-3650 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-12-5299         TCGA-14-0781         TCGA-14-0787 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-14-0789         TCGA-14-0790         TCGA-14-0817 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-14-1034         TCGA-14-1823         TCGA-14-1825 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-14-1829         TCGA-14-2554         TCGA-15-0742 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-15-1444         TCGA-16-0846         TCGA-16-1045 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2620 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-19-2624         TCGA-19-2625         TCGA-19-4065 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-26-5136         TCGA-26-5139         TCGA-27-1830 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1834 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-27-1835         TCGA-27-1837         TCGA-27-2519 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-27-2521         TCGA-27-2523         TCGA-27-2524 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-27-2526         TCGA-27-2528         TCGA-28-1747 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-1753         TCGA-28-2509         TCGA-28-2510 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-2513         TCGA-28-2514         TCGA-28-5204 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-5213         TCGA-28-5215         TCGA-28-5216 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-5218         TCGA-28-5220         TCGA-32-1970 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-76-4931 
"20P LOSS WILD-TYPE" 
D75V10, multiclass
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2569         TCGA-06-2570 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-08-0386         TCGA-12-0616         TCGA-12-0618 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-12-0619         TCGA-12-0821         TCGA-12-3650 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-12-5299         TCGA-14-0781         TCGA-14-0787 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-14-0789         TCGA-14-0790         TCGA-14-0817 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-14-1034         TCGA-14-1823         TCGA-14-1825 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-14-1829         TCGA-14-2554         TCGA-15-0742 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-15-1444         TCGA-16-0846         TCGA-16-1045 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2620 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-19-2624         TCGA-19-2625         TCGA-19-4065 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-26-5136         TCGA-26-5139         TCGA-27-1830 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1834 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-27-1835         TCGA-27-1837         TCGA-27-2519 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-27-2521         TCGA-27-2523         TCGA-27-2524 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-27-2526         TCGA-27-2528         TCGA-28-1747 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-1753         TCGA-28-2509         TCGA-28-2510 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-2513         TCGA-28-2514         TCGA-28-5204 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-5213         TCGA-28-5215         TCGA-28-5216 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-28-5218         TCGA-28-5220         TCGA-32-1970 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-76-4931 
"20P LOSS WILD-TYPE" 

Clustering(76) Variable = 20q loss mutation analysis
D76V1, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                4                168
  CLUS_2                5                165
  CLUS_3                0                167
D76V2, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                4                213
  CLUS_2                0                126
  CLUS_3                5                161
D76V3, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                1                138
  CLUS_2                3                154
  CLUS_3                2                 70
  CLUS_4                2                102
D76V4, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                2                161
  CLUS_2                2                177
  CLUS_3                4                126
D76V5, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                7                154
  CLUS_2                1                213
  CLUS_3                2                186
D76V6, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                107 
        TCGA-06-0650         TCGA-06-1804         TCGA-06-1806 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-6388         TCGA-06-6389         TCGA-06-6390 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-6391         TCGA-06-6693         TCGA-06-6694 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-6695         TCGA-06-6697         TCGA-06-6698 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-6699         TCGA-06-6700         TCGA-06-6701 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-12-5295         TCGA-12-5299         TCGA-12-5301 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-14-0740         TCGA-14-0781         TCGA-14-0862 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-14-1043         TCGA-14-1395         TCGA-14-1450 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-15-1444         TCGA-19-4065         TCGA-19-5947 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-19-5950         TCGA-19-5951         TCGA-19-5952 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-19-5953         TCGA-19-5954         TCGA-19-5955 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-19-5956         TCGA-19-5958         TCGA-19-5959 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-26-5136         TCGA-26-5139         TCGA-26-6173 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-26-6174         TCGA-28-2501         TCGA-28-2510 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-5204         TCGA-28-5207         TCGA-28-5208 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-5209         TCGA-28-5211         TCGA-28-5213 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-5214         TCGA-28-5215         TCGA-28-5216 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-5218         TCGA-28-5219         TCGA-28-5220 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-6450         TCGA-32-1979         TCGA-32-1980 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-32-5222         TCGA-41-5651         TCGA-41-6646 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-74-6573         TCGA-74-6575         TCGA-74-6577 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-74-6578         TCGA-74-6581         TCGA-74-6584 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-76-4925         TCGA-76-4926         TCGA-76-4928 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-76-4929         TCGA-76-4931         TCGA-76-4934 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-76-4935         TCGA-76-6191         TCGA-76-6192 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-76-6193         TCGA-76-6280         TCGA-76-6282 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-76-6283         TCGA-76-6656         TCGA-76-6657 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-76-6660         TCGA-76-6661         TCGA-76-6662 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-76-6663         TCGA-76-6664         TCGA-81-5910 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-81-5911         TCGA-87-5896 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D76V7, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                2                 52
  CLUS_2                2                 56
  CLUS_3                0                 44
  CLUS_4                0                 45
D76V8, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                0                 64
  CLUS_2                1                 32
  CLUS_3                3                101
D76V9, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2569         TCGA-06-2570 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-08-0386         TCGA-12-0616         TCGA-12-0618 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-12-0619         TCGA-12-0821         TCGA-12-3650 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-12-5299         TCGA-14-0781         TCGA-14-0787 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-14-0789         TCGA-14-0790         TCGA-14-0817 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-14-1034         TCGA-14-1823         TCGA-14-1825 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-14-1829         TCGA-14-2554         TCGA-15-0742 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-15-1444         TCGA-16-0846         TCGA-16-1045 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2620 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-19-2624         TCGA-19-2625         TCGA-19-4065 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-26-5136         TCGA-26-5139         TCGA-27-1830 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1834 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-27-1835         TCGA-27-1837         TCGA-27-2519 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-27-2521         TCGA-27-2523         TCGA-27-2524 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-27-2526         TCGA-27-2528         TCGA-28-1747 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-1753         TCGA-28-2509         TCGA-28-2510 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-2513         TCGA-28-2514         TCGA-28-5204 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-5213         TCGA-28-5215         TCGA-28-5216 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-5218         TCGA-28-5220         TCGA-32-1970 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-76-4931 
"20Q LOSS WILD-TYPE" 
D76V10, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                145 
        TCGA-02-0047         TCGA-02-0055         TCGA-02-2483 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-02-2485         TCGA-02-2486         TCGA-06-0125 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0129         TCGA-06-0130         TCGA-06-0132 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0138         TCGA-06-0141         TCGA-06-0157 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0158         TCGA-06-0168         TCGA-06-0174 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0178         TCGA-06-0184         TCGA-06-0187 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0190         TCGA-06-0210         TCGA-06-0211 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0219         TCGA-06-0238         TCGA-06-0644 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0645         TCGA-06-0646         TCGA-06-0649 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0686         TCGA-06-0743         TCGA-06-0744 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0745         TCGA-06-0747         TCGA-06-0749 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-0750         TCGA-06-0878         TCGA-06-0882 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-1804         TCGA-06-2557         TCGA-06-2558 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-2559         TCGA-06-2561         TCGA-06-2562 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-2563         TCGA-06-2564         TCGA-06-2565 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-2567         TCGA-06-2569         TCGA-06-2570 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-5408         TCGA-06-5410         TCGA-06-5411 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-5412         TCGA-06-5413         TCGA-06-5414 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-5415         TCGA-06-5416         TCGA-06-5418 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-06-5856         TCGA-06-5858         TCGA-06-5859 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-08-0386         TCGA-12-0616         TCGA-12-0618 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-12-0619         TCGA-12-0821         TCGA-12-3650 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-12-3652         TCGA-12-3653         TCGA-12-5295 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-12-5299         TCGA-14-0781         TCGA-14-0787 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-14-0789         TCGA-14-0790         TCGA-14-0817 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-14-1034         TCGA-14-1823         TCGA-14-1825 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-14-1829         TCGA-14-2554         TCGA-15-0742 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-15-1444         TCGA-16-0846         TCGA-16-1045 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-19-1787         TCGA-19-2619         TCGA-19-2620 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-19-2624         TCGA-19-2625         TCGA-19-4065 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-19-5960         TCGA-26-1442         TCGA-26-5132 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-26-5133         TCGA-26-5134         TCGA-26-5135 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-26-5136         TCGA-26-5139         TCGA-27-1830 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-27-1831         TCGA-27-1832         TCGA-27-1834 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-27-1835         TCGA-27-1837         TCGA-27-2519 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-27-2521         TCGA-27-2523         TCGA-27-2524 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-27-2526         TCGA-27-2528         TCGA-28-1747 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-1753         TCGA-28-2509         TCGA-28-2510 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-2513         TCGA-28-2514         TCGA-28-5204 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-5207         TCGA-28-5208         TCGA-28-5209 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-5213         TCGA-28-5215         TCGA-28-5216 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-28-5218         TCGA-28-5220         TCGA-32-1970 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-32-1980         TCGA-32-1982         TCGA-32-2615 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-32-2616         TCGA-32-2632         TCGA-32-2634 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-32-2638         TCGA-32-4213         TCGA-32-5222 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-41-2571         TCGA-41-2572         TCGA-41-3915 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-41-4097         TCGA-41-5651         TCGA-76-4925 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-76-4926         TCGA-76-4928         TCGA-76-4929 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-76-4931 
"20Q LOSS WILD-TYPE" 

Clustering(77) Variable = 21q loss mutation analysis
D77V1, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                3                169
  CLUS_2               14                156
  CLUS_3                6                161
D77V2, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                5                212
  CLUS_2                4                122
  CLUS_3               14                152
D77V3, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                3                136
  CLUS_2               12                145
  CLUS_3                5                 67
  CLUS_4                3                101
D77V4, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                5                158
  CLUS_2                5                174
  CLUS_3               13                117
D77V5, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               12                149
  CLUS_2                4                210
  CLUS_3                9                179
D77V6, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                0                 38
  CLUS_2                1                 19
  CLUS_3                2                 22
  CLUS_4                2                 25
D77V7, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                0                 54
  CLUS_2                3                 55
  CLUS_3                4                 40
  CLUS_4                0                 45
D77V8, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                4                 60
  CLUS_2                0                 33
  CLUS_3                3                101
D77V9, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                 42
  CLUS_2                3                 64
  CLUS_3                0                 36
D77V10, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                 64
  CLUS_2                1                 20
  CLUS_3                2                 58

Clustering(78) Variable = 22q loss mutation analysis
D78V1, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               47                125
  CLUS_2               42                128
  CLUS_3               41                126
D78V2, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               56                161
  CLUS_2               32                 94
  CLUS_3               42                124
D78V3, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               35                104
  CLUS_2               46                111
  CLUS_3               17                 55
  CLUS_4               22                 82
D78V4, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               43                120
  CLUS_2               46                133
  CLUS_3               31                 99
D78V5, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               60                101
  CLUS_2               43                171
  CLUS_3               37                151
D78V6, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               10                 28
  CLUS_2                9                 11
  CLUS_3                7                 17
  CLUS_4                5                 22
D78V7, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               13                 41
  CLUS_2               18                 40
  CLUS_3               15                 29
  CLUS_4               13                 32
D78V8, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               18                 46
  CLUS_2               10                 23
  CLUS_3               31                 73
D78V9, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               12                 32
  CLUS_2               18                 49
  CLUS_3               16                 20
D78V10, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               22                 44
  CLUS_2                6                 15
  CLUS_3               18                 42

Clustering(79) Variable = Xq loss mutation analysis
D79V1, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               2               170
  CLUS_2               4               166
  CLUS_3               5               162
D79V2, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               3               214
  CLUS_2               4               122
  CLUS_3               4               162
D79V3, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1               138
  CLUS_2               4               153
  CLUS_3               4                68
  CLUS_4               1               103
D79V4, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               2               161
  CLUS_2               6               173
  CLUS_3               2               128
D79V5, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               6               155
  CLUS_2               2               212
  CLUS_3               3               185
D79V6, multiclass
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2               107 
       TCGA-06-0650        TCGA-06-1804        TCGA-06-1806        TCGA-06-5408 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5416        TCGA-06-5418 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-06-6388 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-06-6389        TCGA-06-6390        TCGA-06-6391        TCGA-06-6693 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-06-6694        TCGA-06-6695        TCGA-06-6697        TCGA-06-6698 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-06-6699        TCGA-06-6700        TCGA-06-6701        TCGA-12-5295 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-12-5299        TCGA-12-5301        TCGA-14-0740        TCGA-14-0781 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-14-0862        TCGA-14-1043        TCGA-14-1395        TCGA-14-1450 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-15-1444        TCGA-19-4065        TCGA-19-5950        TCGA-19-5951 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-19-5952        TCGA-19-5953        TCGA-19-5954        TCGA-19-5955 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-19-5956        TCGA-19-5958        TCGA-19-5959        TCGA-19-5960 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-26-1442        TCGA-26-5132        TCGA-26-5133        TCGA-26-5134 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-26-5135        TCGA-26-5136        TCGA-26-5139        TCGA-26-6173 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-26-6174        TCGA-28-2501        TCGA-28-2510        TCGA-28-5204 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-28-5207        TCGA-28-5208        TCGA-28-5209        TCGA-28-5211 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-28-5213        TCGA-28-5214        TCGA-28-5215        TCGA-28-5216 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-28-5218        TCGA-28-5219        TCGA-28-5220        TCGA-28-6450 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-32-1979        TCGA-32-1980        TCGA-32-5222        TCGA-41-5651 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-41-6646        TCGA-74-6573        TCGA-74-6575        TCGA-74-6577 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-74-6578        TCGA-74-6581        TCGA-74-6584        TCGA-76-4925 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-76-4928        TCGA-76-4929        TCGA-76-4931        TCGA-76-4934 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-76-4935        TCGA-76-6191        TCGA-76-6192        TCGA-76-6193 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-76-6280        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-76-6286        TCGA-76-6656        TCGA-76-6657        TCGA-76-6660 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-76-6661        TCGA-76-6662        TCGA-76-6663        TCGA-76-6664 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-81-5910        TCGA-81-5911        TCGA-87-5896 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D79V7, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               2                52
  CLUS_2               2                56
  CLUS_3               2                42
  CLUS_4               0                45
D79V8, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               2                62
  CLUS_2               2                31
  CLUS_3               2               102
D79V9, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               2                42
  CLUS_2               1                66
  CLUS_3               2                34
D79V10, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                65
  CLUS_2               1                20
  CLUS_3               3                57
                     V1                      V2                      V3 
            "MRNA_CNMF"    "MRNA_CHIERARCHICAL"              "MIR_CNMF" 
                     V4                      V5                      V6 
    "MIR_CHIERARCHICAL"               "CN_CNMF"      "METHLYATION_CNMF" 
                     V7                      V8                      V9 
            "RPPA_CNMF"    "RPPA_CHIERARCHICAL"          "MRNASEQ_CNMF" 
                    V10 
"MRNASEQ_CHIERARCHICAL" 
> q(save="no")
