
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/376240/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/UCEC-TP/2909297/1.GDAC_mergedClustering.Finished/UCEC-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=UCEC-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=UCEC-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=500, in cluster file=492, common to both=492
[1] "Reduce the number of clustering variables from 80 to 79."
[1]  79 492
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               21               471 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               21               471 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              138               354 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              138               354 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               51               441 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               51               441 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               40               452 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               40               452 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               28               464 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               28               464 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               50               442 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               50               442 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                6               486 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                6               486 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               32               460 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               32               460 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                9               483 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                9               483 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               38               454 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               38               454 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               30               462 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               30               462 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               43               449 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               43               449 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               43               449 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               43               449 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               86               406 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               86               406 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              118               374 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              118               374 
[1] "9p gain mutation analysis"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               14               478 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               14               478 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4               488 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4               488 
[1] "10p gain mutation analysis"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                87                405 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                87                405 
[1] "10q gain mutation analysis"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                79                413 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                79                413 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 8                484 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 8                484 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 8                484 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 8                484 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                37                455 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                37                455 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                28                464 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                28                464 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                20                472 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                20                472 
[1] "14q gain mutation analysis"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                20                472 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                20                472 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 6                486 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 6                486 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                12                480 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                12                480 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 4                488 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 4                488 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 7                485 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 7                485 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                13                479 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                13                479 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                37                455 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                37                455 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                20                472 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                20                472 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                31                461 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                31                461 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                28                464 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                28                464 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                65                427 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                65                427 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                78                414 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                78                414 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                25                467 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                25                467 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 9                483 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 9                483 
[1] "Xq gain mutation analysis"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               12               480 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               12               480 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               13               479 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               13               479 
[1] "1q loss mutation analysis"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4               488 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4               488 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                6               486 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                6               486 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                8               484 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                8               484 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               31               461 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               31               461 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               12               480 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               12               480 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               66               426 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               66               426 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               64               428 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               64               428 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               27               465 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               27               465 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               45               447 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               45               447 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               10               482 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               10               482 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               12               480 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               12               480 
[1] "7p loss mutation analysis"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               29               463 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               29               463 
[1] "7q loss mutation analysis"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               27               465 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               27               465 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               53               439 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               53               439 
[1] "8q loss mutation analysis"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               12               480 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               12               480 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               76               416 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               76               416 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               93               399 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               93               399 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                23                469 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                23                469 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                24                468 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                24                468 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                53                439 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                53                439 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                45                447 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                45                447 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                25                467 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                25                467 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                18                474 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                18                474 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                60                432 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                60                432 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                42                450 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                42                450 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                81                411 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                81                411 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                69                423 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                69                423 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               110                382 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               110                382 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               105                387 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               105                387 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                68                424 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                68                424 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                36                456 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                36                456 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                49                443 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                49                443 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                34                458 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                34                458 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                28                464 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                28                464 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                15                477 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                15                477 
[1] "20q loss mutation analysis"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 7                485 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 7                485 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                32                460 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                32                460 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                87                405 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                87                405 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               18               474 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               18               474 
[1] "data2feature, selection=ALL"
 [1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
 [4] "METHLYATION_CNMF"      "RPPA_CNMF"             "RPPA_CHIERARCHICAL"   
 [7] "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"          
[10] "MIRSEQ_CHIERARCHICAL" 

Input Data has 10 rows and 492 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'RPPA_CNMF':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
 [4] "METHLYATION_CNMF"      "RPPA_CNMF"             "RPPA_CHIERARCHICAL"   
 [7] "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"          
[10] "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 492 columns, 0 survival variables, and 10 non-survival variables.
MRNA_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
CN_CNMF, nv=5, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=6, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=2, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=6, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain mutation analysis
D1V1, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1                12
  CLUS_2               2                16
  CLUS_3               0                14
  CLUS_4               0                 8
D1V2, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               0                20
  CLUS_2               2                13
  CLUS_3               1                17
D1V3, multiclass
D1V4, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               8               135
  CLUS_2               4                81
  CLUS_3               5               144
D1V5, multiclass
D1V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      3    2
  1P GAIN WILD-TYPE  118   71
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               3               118
  CLUS_2               2                71
D1V7, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               7               135
  CLUS_2               1               106
  CLUS_3               3               110
D1V8, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1                64
  CLUS_2               1                91
  CLUS_3               4                61
  CLUS_4               5               135
D1V9, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              14               180
  CLUS_2               2               144
  CLUS_3               5               134
D1V10, multiclass

Clustering(2) Variable = 1q gain mutation analysis
D2V1, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               8                 5
  CLUS_2               5                13
  CLUS_3               6                 8
  CLUS_4               1                 7
D2V2, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               6                14
  CLUS_2               7                 8
  CLUS_3               7                11
D2V3, multiclass
D2V4, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              24               119
  CLUS_2              19                66
  CLUS_3              49               100
D2V5, multiclass
D2V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     48   12
  1Q GAIN WILD-TYPE   73   61
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              48                73
  CLUS_2              12                61
D2V7, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              24               118
  CLUS_2              26                81
  CLUS_3              51                62
D2V8, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              26                39
  CLUS_2              24                68
  CLUS_3              31                34
  CLUS_4              20               120
D2V9, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              33               161
  CLUS_2              35               111
  CLUS_3              67                72
D2V10, multiclass

Clustering(3) Variable = 2p gain mutation analysis
D3V1, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               0                13
  CLUS_2               3                15
  CLUS_3               3                11
  CLUS_4               0                 8
D3V2, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               3                17
  CLUS_2               0                15
  CLUS_3               3                15
D3V3, multiclass
D3V4, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              19               124
  CLUS_2               7                78
  CLUS_3               8               141
D3V5, multiclass
D3V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     12    6
  2P GAIN WILD-TYPE  109   67
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              12               109
  CLUS_2               6                67
D3V7, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              19               123
  CLUS_2               8                99
  CLUS_3               9               104
D3V8, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               7                58
  CLUS_2               6                86
  CLUS_3               5                60
  CLUS_4              18               122
D3V9, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              29               165
  CLUS_2               9               137
  CLUS_3              11               128
D3V10, multiclass

Clustering(4) Variable = 2q gain mutation analysis
D4V1, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               0                13
  CLUS_2               1                17
  CLUS_3               2                12
  CLUS_4               0                 8
D4V2, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               2                18
  CLUS_2               0                15
  CLUS_3               1                17
D4V3, multiclass
D4V4, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              15               128
  CLUS_2               6                79
  CLUS_3               7               142
D4V5, multiclass
D4V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     10    4
  2Q GAIN WILD-TYPE  111   69
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              10               111
  CLUS_2               4                69
D4V7, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              14               128
  CLUS_2               6               101
  CLUS_3               6               107
D4V8, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               5                60
  CLUS_2               5                87
  CLUS_3               3                62
  CLUS_4              13               127
D4V9, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              24               170
  CLUS_2               7               139
  CLUS_3               8               131
D4V10, multiclass

Clustering(5) Variable = 3p gain mutation analysis
D5V1, multiclass
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B5-A0JR        TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D5V2, multiclass
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B5-A0JR        TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D5V3, multiclass
D5V4, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              13               130
  CLUS_2               5                80
  CLUS_3               5               144
D5V5, multiclass
D5V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      4    1
  3P GAIN WILD-TYPE  117   72
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               4               117
  CLUS_2               1                72
D5V7, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              12               130
  CLUS_2               6               101
  CLUS_3               1               112
D5V8, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               0                65
  CLUS_2               3                89
  CLUS_3               5                60
  CLUS_4              11               129
D5V9, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              12               182
  CLUS_2               7               139
  CLUS_3               8               131
D5V10, multiclass

Clustering(6) Variable = 3q gain mutation analysis
D6V1, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               0                13
  CLUS_2               3                15
  CLUS_3               0                14
  CLUS_4               0                 8
D6V2, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               0                20
  CLUS_2               0                15
  CLUS_3               3                15
D6V3, multiclass
D6V4, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              29               114
  CLUS_2               6                79
  CLUS_3               6               143
D6V5, multiclass
D6V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      4    5
  3Q GAIN WILD-TYPE  117   68
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               4               117
  CLUS_2               5                68
D6V7, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              26               116
  CLUS_2               6               101
  CLUS_3               1               112
D6V8, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               0                65
  CLUS_2               3                89
  CLUS_3               7                58
  CLUS_4              23               117
D6V9, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              32               162
  CLUS_2               8               138
  CLUS_3               9               130
D6V10, multiclass

Clustering(7) Variable = 4p gain mutation analysis
D7V1, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GE 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP        TCGA-A5-A0GU 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V2, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GE 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP        TCGA-A5-A0GU 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V3, multiclass
D7V4, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               2               141
  CLUS_2               2                83
  CLUS_3               0               149
D7V5, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G9        TCGA-A5-A0GA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE        TCGA-A5-A0GG 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ        TCGA-A5-A0GM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR        TCGA-A5-A0GU 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX        TCGA-A5-A0R6 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9        TCGA-A5-A0RA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051        TCGA-AP-A052 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A059 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H        TCGA-AP-A05J 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P        TCGA-AP-A0LD 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG        TCGA-AP-A0LH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL        TCGA-AP-A0LM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT        TCGA-AP-A0LV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06D 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L        TCGA-AX-A0IS 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0        TCGA-AX-A0J1 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B5-A0JN        TCGA-B5-A0JT        TCGA-B5-A0JY        TCGA-B5-A0JZ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K2        TCGA-B5-A0K3 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B5-A0K4        TCGA-B5-A0K7        TCGA-B5-A0K9        TCGA-B5-A11E 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B5-A11F        TCGA-B5-A11G        TCGA-B5-A11H        TCGA-B5-A11I 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B5-A11N        TCGA-B5-A11Q        TCGA-B5-A11S        TCGA-B5-A11U 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B5-A11V        TCGA-B5-A11W        TCGA-B5-A11Y        TCGA-B5-A11Z 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B5-A121        TCGA-BG-A0LW        TCGA-BG-A0LX        TCGA-BG-A0M0 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BG-A0M2        TCGA-BG-A0M3        TCGA-BG-A0M4        TCGA-BG-A0M7 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BG-A0M8        TCGA-BG-A0M9        TCGA-BG-A0MC        TCGA-BG-A0MG 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BG-A0MS        TCGA-BG-A0MT        TCGA-BG-A0MU        TCGA-BG-A0RY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BG-A0VT        TCGA-BG-A0VV        TCGA-BG-A0W1        TCGA-BG-A0YU 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BG-A0YV        TCGA-BG-A186        TCGA-BG-A187        TCGA-BG-A18A 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BG-A18B        TCGA-BG-A18C        TCGA-BK-A0C9        TCGA-BK-A0CA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139        TCGA-BK-A13C 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC        TCGA-BS-A0TD 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ        TCGA-BS-A0U7 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BS-A0U8        TCGA-BS-A0U9        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    2
  4P GAIN WILD-TYPE  121   71
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0               121
  CLUS_2               2                71
D7V7, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               4               138
  CLUS_2               0               107
  CLUS_3               0               113
D7V8, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0                65
  CLUS_2               0                92
  CLUS_3               0                65
  CLUS_4               4               136
D7V9, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               6               188
  CLUS_2               0               146
  CLUS_3               0               139
D7V10, multiclass

Clustering(8) Variable = 5p gain mutation analysis
D8V1, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               0                13
  CLUS_2               2                16
  CLUS_3               1                13
  CLUS_4               0                 8
D8V2, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               1                19
  CLUS_2               0                15
  CLUS_3               2                16
D8V3, multiclass
D8V4, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              20               123
  CLUS_2               3                82
  CLUS_3               3               146
D8V5, multiclass
D8V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      6    2
  5P GAIN WILD-TYPE  115   71
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               6               115
  CLUS_2               2                71
D8V7, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              19               123
  CLUS_2               0               107
  CLUS_3               3               110
D8V8, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                63
  CLUS_2               0                92
  CLUS_3               3                62
  CLUS_4              17               123
D8V9, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              24               170
  CLUS_2               1               145
  CLUS_3               6               133
D8V10, multiclass

Clustering(9) Variable = 5q gain mutation analysis
D9V1, multiclass
D9V2, multiclass
D9V3, multiclass
D9V4, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               5               138
  CLUS_2               1                84
  CLUS_3               2               147
D9V5, multiclass
[1] "Remove cluster labels:" "5Q GAIN MUTATED"       
clus
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                1               193 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0G9 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A5-A0GG        TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A5-A0GM        TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A5-A0R6        TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A5-A0RA        TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AP-A059        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AP-A0LM        TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AX-A06D        TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0        TCGA-AX-A0J1 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B5-A0JN        TCGA-B5-A0JT        TCGA-B5-A0JY        TCGA-B5-A0JZ 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K2        TCGA-B5-A0K3 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B5-A0K4        TCGA-B5-A0K7        TCGA-B5-A0K9        TCGA-B5-A11E 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B5-A11F        TCGA-B5-A11G        TCGA-B5-A11H        TCGA-B5-A11I 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B5-A11N        TCGA-B5-A11Q        TCGA-B5-A11S        TCGA-B5-A11U 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B5-A11V        TCGA-B5-A11W        TCGA-B5-A11Y        TCGA-B5-A11Z 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B5-A121        TCGA-BG-A0LW        TCGA-BG-A0LX        TCGA-BG-A0M0 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BG-A0M2        TCGA-BG-A0M3        TCGA-BG-A0M4        TCGA-BG-A0M6 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BG-A0M7        TCGA-BG-A0M8        TCGA-BG-A0M9        TCGA-BG-A0MC 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BG-A0MG        TCGA-BG-A0MS        TCGA-BG-A0MT        TCGA-BG-A0MU 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BG-A0RY        TCGA-BG-A0VT        TCGA-BG-A0VV        TCGA-BG-A0W1 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BG-A0YU        TCGA-BG-A0YV        TCGA-BG-A186        TCGA-BG-A187 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BG-A18A        TCGA-BG-A18B        TCGA-BG-A18C        TCGA-BK-A0C9 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BK-A0CA        TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BK-A13C        TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BS-A0TD        TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BS-A0U7        TCGA-BS-A0U8        TCGA-BS-A0U9        TCGA-BS-A0UF 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BS-A0UJ        TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D1-A0ZU        TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D1-A103        TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D1-A15Z        TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D1-A165        TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D1-A16B        TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D1-A16I        TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D1-A16Q        TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D1-A16X        TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D1-A177        TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D1-A17D        TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D1-A17L        TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D1-A17R        TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DI-A0WH 
"5Q GAIN WILD-TYPE" 
D9V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1    0
  5Q GAIN WILD-TYPE  120   73
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1               120
  CLUS_2               0                73
D9V7, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               6               136
  CLUS_2               0               107
  CLUS_3               2               111
D9V8, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1                64
  CLUS_2               0                92
  CLUS_3               2                63
  CLUS_4               5               135
D9V9, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               7               187
  CLUS_2               0               146
  CLUS_3               2               137
D9V10, multiclass

Clustering(10) Variable = 6p gain mutation analysis
D10V1, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               0                13
  CLUS_2               3                15
  CLUS_3               1                13
  CLUS_4               0                 8
D10V2, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1                19
  CLUS_2               0                15
  CLUS_3               3                15
D10V3, multiclass
D10V4, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              19               124
  CLUS_2               7                78
  CLUS_3               7               142
D10V5, multiclass
D10V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      4    2
  6P GAIN WILD-TYPE  117   71
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               4               117
  CLUS_2               2                71
D10V7, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              16               126
  CLUS_2               5               102
  CLUS_3               2               111
D10V8, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               0                65
  CLUS_2               4                88
  CLUS_3               3                62
  CLUS_4              16               124
D10V9, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              24               170
  CLUS_2               8               138
  CLUS_3               5               134
D10V10, multiclass

Clustering(11) Variable = 6q gain mutation analysis
D11V1, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               0                13
  CLUS_2               3                15
  CLUS_3               1                13
  CLUS_4               0                 8
D11V2, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               1                19
  CLUS_2               0                15
  CLUS_3               3                15
D11V3, multiclass
D11V4, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              13               130
  CLUS_2               5                80
  CLUS_3               7               142
D11V5, multiclass
D11V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3    2
  6Q GAIN WILD-TYPE  118   71
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               3               118
  CLUS_2               2                71
D11V7, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              15               127
  CLUS_2               4               103
  CLUS_3               2               111
D11V8, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               0                65
  CLUS_2               3                89
  CLUS_3               3                62
  CLUS_4              15               125
D11V9, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              17               177
  CLUS_2               7               139
  CLUS_3               5               134
D11V10, multiclass

Clustering(12) Variable = 7p gain mutation analysis
D12V1, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               1                12
  CLUS_2               2                16
  CLUS_3               2                12
  CLUS_4               1                 7
D12V2, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               3                17
  CLUS_2               1                14
  CLUS_3               2                16
D12V3, multiclass
D12V4, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              16               127
  CLUS_2               1                84
  CLUS_3              11               138
D12V5, multiclass
D12V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     10    2
  7P GAIN WILD-TYPE  111   71
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              10               111
  CLUS_2               2                71
D12V7, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               9               133
  CLUS_2               7               100
  CLUS_3               7               106
D12V8, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               6                59
  CLUS_2               6                86
  CLUS_3               5                60
  CLUS_4               6               134
D12V9, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              18               176
  CLUS_2               9               137
  CLUS_3              14               125
D12V10, multiclass

Clustering(13) Variable = 7q gain mutation analysis
D13V1, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               1                12
  CLUS_2               3                15
  CLUS_3               2                12
  CLUS_4               1                 7
D13V2, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               3                17
  CLUS_2               1                14
  CLUS_3               3                15
D13V3, multiclass
D13V4, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              13               130
  CLUS_2               1                84
  CLUS_3              14               135
D13V5, multiclass
D13V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     10    1
  7Q GAIN WILD-TYPE  111   72
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              10               111
  CLUS_2               1                72
D13V7, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               6               136
  CLUS_2               8                99
  CLUS_3               9               104
D13V8, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               9                56
  CLUS_2               6                86
  CLUS_3               4                61
  CLUS_4               4               136
D13V9, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              16               178
  CLUS_2              11               135
  CLUS_3              14               125
D13V10, multiclass

Clustering(14) Variable = 8p gain mutation analysis
D14V1, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               0                13
  CLUS_2               3                15
  CLUS_3               2                12
  CLUS_4               0                 8
D14V2, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               2                18
  CLUS_2               1                14
  CLUS_3               2                16
D14V3, multiclass
D14V4, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              27               116
  CLUS_2              14                71
  CLUS_3              28               121
D14V5, multiclass
D14V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     18   11
  8P GAIN WILD-TYPE  103   62
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              18               103
  CLUS_2              11                62
D14V7, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              27               115
  CLUS_2              14                93
  CLUS_3              19                94
D14V8, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              10                55
  CLUS_2              12                80
  CLUS_3               9                56
  CLUS_4              29               111
D14V9, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              36               158
  CLUS_2              21               125
  CLUS_3              27               112
D14V10, multiclass

Clustering(15) Variable = 8q gain mutation analysis
D15V1, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               0                13
  CLUS_2               8                10
  CLUS_3               2                12
  CLUS_4               0                 8
D15V2, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2                18
  CLUS_2               1                14
  CLUS_3               7                11
D15V3, multiclass
D15V4, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              41               102
  CLUS_2              21                64
  CLUS_3              32               117
D15V5, multiclass
D15V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     25   15
  8Q GAIN WILD-TYPE   96   58
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              25                96
  CLUS_2              15                58
D15V7, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              43                99
  CLUS_2              16                91
  CLUS_3              19                94
D15V8, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              10                55
  CLUS_2              12                80
  CLUS_3               9                56
  CLUS_4              47                93
D15V9, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              62               132
  CLUS_2              26               120
  CLUS_3              26               113
D15V10, multiclass

Clustering(16) Variable = 9p gain mutation analysis
D16V1, multiclass
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A060        TCGA-AX-A062 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
D16V2, multiclass
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A060        TCGA-AX-A062 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
D16V3, multiclass
D16V4, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               9               134
  CLUS_2               1                84
  CLUS_3               3               146
D16V5, multiclass
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0G9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0GG        TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0GM        TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0R6        TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0RA        TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A059        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0LM        TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A060        TCGA-AX-A062 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L        TCGA-AX-A0IS 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0        TCGA-AX-A0J1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B5-A0JN        TCGA-B5-A0JT        TCGA-B5-A0JY        TCGA-B5-A0JZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K2        TCGA-B5-A0K3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B5-A0K4        TCGA-B5-A0K7        TCGA-B5-A0K9        TCGA-B5-A11E 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B5-A11F        TCGA-B5-A11G        TCGA-B5-A11I        TCGA-B5-A11N 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B5-A11Q        TCGA-B5-A11S        TCGA-B5-A11U        TCGA-B5-A11V 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B5-A11W        TCGA-B5-A11Y        TCGA-B5-A11Z        TCGA-B5-A121 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0LX        TCGA-BG-A0M0        TCGA-BG-A0M2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BG-A0M3        TCGA-BG-A0M4        TCGA-BG-A0M6        TCGA-BG-A0M7 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BG-A0M8        TCGA-BG-A0M9        TCGA-BG-A0MC        TCGA-BG-A0MG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BG-A0MS        TCGA-BG-A0MT        TCGA-BG-A0MU        TCGA-BG-A0RY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BG-A0VT        TCGA-BG-A0VV        TCGA-BG-A0W1        TCGA-BG-A0YU 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BG-A0YV        TCGA-BG-A186        TCGA-BG-A187        TCGA-BG-A18A 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BG-A18B        TCGA-BG-A18C        TCGA-BK-A0C9        TCGA-BK-A0CA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139        TCGA-BK-A13C 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC        TCGA-BS-A0TD 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ        TCGA-BS-A0U7 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BS-A0U8        TCGA-BS-A0U9        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
D16V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1    1
  9P GAIN WILD-TYPE  120   72
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               1               120
  CLUS_2               1                72
D16V7, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               4               138
  CLUS_2               2               105
  CLUS_3               2               111
D16V8, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               0                65
  CLUS_2               0                92
  CLUS_3               2                63
  CLUS_4               6               134
D16V9, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              10               184
  CLUS_2               1               145
  CLUS_3               3               136
D16V10, multiclass

Clustering(17) Variable = 9q gain mutation analysis
D17V1, multiclass
D17V2, multiclass
D17V3, multiclass
D17V4, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               3               140
  CLUS_2               0                85
  CLUS_3               1               148
D17V5, multiclass
D17V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0    0
  9Q GAIN WILD-TYPE  121   73
D17V7, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2               140
  CLUS_2               0               107
  CLUS_3               1               112
D17V8, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               0                65
  CLUS_2               0                92
  CLUS_3               0                65
  CLUS_4               3               137
D17V9, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               3               191
  CLUS_2               0               146
  CLUS_3               1               138
D17V10, multiclass

Clustering(18) Variable = 10p gain mutation analysis
D18V1, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                3                 15
  CLUS_3                9                  5
  CLUS_4                1                  7
D18V2, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                9                 11
  CLUS_2                2                 13
  CLUS_3                3                 15
D18V3, multiclass
D18V4, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               17                126
  CLUS_2               14                 71
  CLUS_3               29                120
D18V5, multiclass
D18V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     28   10
  10P GAIN WILD-TYPE   93   63
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               28                 93
  CLUS_2               10                 63
D18V7, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               17                125
  CLUS_2               28                 79
  CLUS_3               19                 94
D18V8, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               15                 50
  CLUS_2               20                 72
  CLUS_3                9                 56
  CLUS_4               20                120
D18V9, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               27                167
  CLUS_2               31                115
  CLUS_3               29                110
D18V10, multiclass

Clustering(19) Variable = 10q gain mutation analysis
D19V1, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                2                 16
  CLUS_3                9                  5
  CLUS_4                1                  7
D19V2, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                9                 11
  CLUS_2                1                 14
  CLUS_3                3                 15
D19V3, multiclass
D19V4, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               15                128
  CLUS_2               12                 73
  CLUS_3               27                122
D19V5, multiclass
D19V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     25   10
  10Q GAIN WILD-TYPE   96   63
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               25                 96
  CLUS_2               10                 63
D19V7, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               16                126
  CLUS_2               26                 81
  CLUS_3               18                 95
D19V8, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               14                 51
  CLUS_2               19                 73
  CLUS_3                8                 57
  CLUS_4               19                121
D19V9, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               21                173
  CLUS_2               30                116
  CLUS_3               28                111
D19V10, multiclass

Clustering(20) Variable = 11p gain mutation analysis
D20V1, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                3                 15
  CLUS_3                0                 14
  CLUS_4                0                  8
D20V2, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                 20
  CLUS_2                0                 15
  CLUS_3                3                 15
D20V3, multiclass
D20V4, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                143
  CLUS_2                3                 82
  CLUS_3                1                148
D20V5, multiclass
D20V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3    1
  11P GAIN WILD-TYPE  118   72
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                3                118
  CLUS_2                1                 72
D20V7, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                4                138
  CLUS_2                1                106
  CLUS_3                0                113
D20V8, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                 65
  CLUS_2                1                 91
  CLUS_3                0                 65
  CLUS_4                4                136
D20V9, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                4                190
  CLUS_2                2                144
  CLUS_3                2                137
D20V10, multiclass

Clustering(21) Variable = 11q gain mutation analysis
D21V1, multiclass
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-BG-A0LW 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D21V2, multiclass
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-BG-A0LW 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D21V3, multiclass
D21V4, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                2                141
  CLUS_2                2                 83
  CLUS_3                1                148
D21V5, multiclass
D21V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      4    0
  11Q GAIN WILD-TYPE  117   73
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                4                117
  CLUS_2                0                 73
D21V7, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                4                138
  CLUS_2                2                105
  CLUS_3                0                113
D21V8, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                 65
  CLUS_2                2                 90
  CLUS_3                0                 65
  CLUS_4                4                136
D21V9, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                4                190
  CLUS_2                3                143
  CLUS_3                1                138
D21V10, multiclass

Clustering(22) Variable = 12p gain mutation analysis
D22V1, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                1                 17
  CLUS_3                2                 12
  CLUS_4                0                  8
D22V2, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                1                 14
  CLUS_3                2                 16
D22V3, multiclass
D22V4, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               16                127
  CLUS_2                8                 77
  CLUS_3                4                145
D22V5, multiclass
D22V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      8    4
  12P GAIN WILD-TYPE  113   69
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                8                113
  CLUS_2                4                 69
D22V7, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               15                127
  CLUS_2                7                100
  CLUS_3                3                110
D22V8, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                 64
  CLUS_2                6                 86
  CLUS_3                3                 62
  CLUS_4               15                125
D22V9, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               23                171
  CLUS_2                7                139
  CLUS_3                7                132
D22V10, multiclass

Clustering(23) Variable = 12q gain mutation analysis
D23V1, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                1                 17
  CLUS_3                2                 12
  CLUS_4                0                  8
D23V2, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                1                 14
  CLUS_3                2                 16
D23V3, multiclass
D23V4, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               10                133
  CLUS_2                7                 78
  CLUS_3                4                145
D23V5, multiclass
D23V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      6    3
  12Q GAIN WILD-TYPE  115   70
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                6                115
  CLUS_2                3                 70
D23V7, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               11                131
  CLUS_2                7                100
  CLUS_3                2                111
D23V8, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                 64
  CLUS_2                6                 86
  CLUS_3                2                 63
  CLUS_4               11                129
D23V9, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               16                178
  CLUS_2                7                139
  CLUS_3                5                134
D23V10, multiclass

Clustering(24) Variable = 13q gain mutation analysis
D24V1, multiclass
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0LD 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LJ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D24V2, multiclass
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0LD 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LJ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D24V3, multiclass
D24V4, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               10                133
  CLUS_2                6                 79
  CLUS_3                1                148
D24V5, multiclass
D24V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2    3
  13Q GAIN WILD-TYPE  119   70
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                2                119
  CLUS_2                3                 70
D24V7, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               13                129
  CLUS_2                1                106
  CLUS_3                0                113
D24V8, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                0                 65
  CLUS_2                1                 91
  CLUS_3                0                 65
  CLUS_4               13                127
D24V9, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               16                178
  CLUS_2                2                144
  CLUS_3                2                137
D24V10, multiclass

Clustering(25) Variable = 14q gain mutation analysis
D25V1, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                1                 17
  CLUS_3                1                 13
  CLUS_4                0                  8
D25V2, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                1                 14
  CLUS_3                1                 17
D25V3, multiclass
D25V4, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               10                133
  CLUS_2                3                 82
  CLUS_3                4                145
D25V5, multiclass
D25V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      3    0
  14Q GAIN WILD-TYPE  118   73
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                3                118
  CLUS_2                0                 73
D25V7, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                5                137
  CLUS_2                3                104
  CLUS_3                1                112
D25V8, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                0                 65
  CLUS_2                2                 90
  CLUS_3                0                 65
  CLUS_4                7                133
D25V9, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               13                181
  CLUS_2                4                142
  CLUS_3                2                137
D25V10, multiclass

Clustering(26) Variable = 15q gain mutation analysis
D26V1, multiclass
D26V2, multiclass
D26V3, multiclass
D26V4, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                1                142
  CLUS_2                1                 84
  CLUS_3                3                146
D26V5, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                193 
        TCGA-A5-A0G1         TCGA-A5-A0G2         TCGA-A5-A0G5 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0G9         TCGA-A5-A0GA         TCGA-A5-A0GB 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0GD         TCGA-A5-A0GE         TCGA-A5-A0GG 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0GH         TCGA-A5-A0GI         TCGA-A5-A0GJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GN         TCGA-A5-A0GQ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0GR         TCGA-A5-A0GU         TCGA-A5-A0GV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0GW         TCGA-A5-A0GX         TCGA-A5-A0R6 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0R7         TCGA-A5-A0R8         TCGA-A5-A0R9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0RA         TCGA-A5-A0VP         TCGA-A5-A0VQ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A059 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A05A         TCGA-AP-A05D         TCGA-AP-A05H 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05O 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0LD         TCGA-AP-A0LE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A0LF         TCGA-AP-A0LG         TCGA-AP-A0LH 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A0LI         TCGA-AP-A0LJ         TCGA-AP-A0LL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A0LM         TCGA-AP-A0LN         TCGA-AP-A0LP 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06D         TCGA-AX-A06F 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A06L         TCGA-AX-A0IS 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A0IW         TCGA-AX-A0IZ         TCGA-AX-A0J0 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JN         TCGA-B5-A0JT 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A0JY         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K2         TCGA-B5-A0K3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-B5-A0K7         TCGA-B5-A0K9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A11E         TCGA-B5-A11F         TCGA-B5-A11G 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A11H         TCGA-B5-A11I         TCGA-B5-A11N 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A11Q         TCGA-B5-A11S         TCGA-B5-A11U 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A11V         TCGA-B5-A11W         TCGA-B5-A11Y 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A11Z         TCGA-B5-A121         TCGA-BG-A0LW 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0LX         TCGA-BG-A0M0         TCGA-BG-A0M2 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0M3         TCGA-BG-A0M4         TCGA-BG-A0M6 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0M7         TCGA-BG-A0M8         TCGA-BG-A0M9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0MC         TCGA-BG-A0MG         TCGA-BG-A0MS 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0MT         TCGA-BG-A0MU         TCGA-BG-A0RY 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0VT         TCGA-BG-A0VV         TCGA-BG-A0W1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0YU         TCGA-BG-A0YV         TCGA-BG-A186 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A187         TCGA-BG-A18A         TCGA-BG-A18B 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A18C         TCGA-BK-A0C9         TCGA-BK-A0CA 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BK-A0CB         TCGA-BK-A0CC         TCGA-BK-A139 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BK-A13C         TCGA-BS-A0T9         TCGA-BS-A0TA 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BS-A0TC         TCGA-BS-A0TD         TCGA-BS-A0TG 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BS-A0TI         TCGA-BS-A0TJ         TCGA-BS-A0U7 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BS-A0U8         TCGA-BS-A0U9         TCGA-BS-A0UF 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BS-A0UJ         TCGA-BS-A0V7         TCGA-D1-A0ZP 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A0ZR         TCGA-D1-A0ZU         TCGA-D1-A0ZZ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A101         TCGA-D1-A103         TCGA-D1-A15V 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A15W         TCGA-D1-A15X         TCGA-D1-A15Z 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A160         TCGA-D1-A161         TCGA-D1-A163 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A165         TCGA-D1-A167         TCGA-D1-A168 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A169         TCGA-D1-A16B         TCGA-D1-A16D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A16E         TCGA-D1-A16G         TCGA-D1-A16I 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A16J         TCGA-D1-A16N         TCGA-D1-A16O 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A16Q         TCGA-D1-A16R         TCGA-D1-A16S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A16V         TCGA-D1-A16X         TCGA-D1-A16Y 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A175         TCGA-D1-A176         TCGA-D1-A177 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A179         TCGA-D1-A17B         TCGA-D1-A17C 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A17D         TCGA-D1-A17F         TCGA-D1-A17H 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A17K         TCGA-D1-A17L         TCGA-D1-A17M 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A17N         TCGA-D1-A17Q         TCGA-D1-A17R 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A17S         TCGA-D1-A17T         TCGA-D1-A17U 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DI-A0WH 
"15Q GAIN WILD-TYPE" 
D26V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1    0
  15Q GAIN WILD-TYPE  120   73
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                1                120
  CLUS_2                0                 73
D26V7, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                1                141
  CLUS_2                1                106
  CLUS_3                2                111
D26V8, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                1                 64
  CLUS_2                0                 92
  CLUS_3                1                 64
  CLUS_4                2                138
D26V9, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                2                192
  CLUS_2                2                144
  CLUS_3                2                137
D26V10, multiclass

Clustering(27) Variable = 16p gain mutation analysis
D27V1, multiclass
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BK-A0CC 
"16P GAIN WILD-TYPE" 
D27V2, multiclass
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BK-A0CC 
"16P GAIN WILD-TYPE" 
D27V3, multiclass
D27V4, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                8                135
  CLUS_2                0                 85
  CLUS_3                3                146
D27V5, multiclass
D27V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3    1
  16P GAIN WILD-TYPE  118   72
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                3                118
  CLUS_2                1                 72
D27V7, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                6                136
  CLUS_2                0                107
  CLUS_3                2                111
D27V8, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                 63
  CLUS_2                0                 92
  CLUS_3                0                 65
  CLUS_4                6                134
D27V9, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                9                185
  CLUS_2                1                145
  CLUS_3                2                137
D27V10, multiclass

Clustering(28) Variable = 16q gain mutation analysis
D28V1, multiclass
D28V2, multiclass
D28V3, multiclass
D28V4, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                142
  CLUS_2                1                 84
  CLUS_3                2                147
D28V5, multiclass
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                193 
        TCGA-A5-A0G1         TCGA-A5-A0G2         TCGA-A5-A0G5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0G9         TCGA-A5-A0GA         TCGA-A5-A0GB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GD         TCGA-A5-A0GE         TCGA-A5-A0GG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GH         TCGA-A5-A0GI         TCGA-A5-A0GJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GN         TCGA-A5-A0GQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GR         TCGA-A5-A0GU         TCGA-A5-A0GV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GW         TCGA-A5-A0GX         TCGA-A5-A0R6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0R7         TCGA-A5-A0R8         TCGA-A5-A0R9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0RA         TCGA-A5-A0VP         TCGA-A5-A0VQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A059 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A05A         TCGA-AP-A05D         TCGA-AP-A05H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05O 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0LD         TCGA-AP-A0LE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LF         TCGA-AP-A0LG         TCGA-AP-A0LH 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LI         TCGA-AP-A0LJ         TCGA-AP-A0LL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LM         TCGA-AP-A0LN         TCGA-AP-A0LP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06D         TCGA-AX-A06F 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A06L         TCGA-AX-A0IS 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A0IW         TCGA-AX-A0IZ         TCGA-AX-A0J0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JN         TCGA-B5-A0JT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0JY         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K2         TCGA-B5-A0K3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-B5-A0K7         TCGA-B5-A0K9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11E         TCGA-B5-A11F         TCGA-B5-A11G 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11H         TCGA-B5-A11I         TCGA-B5-A11N 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11Q         TCGA-B5-A11S         TCGA-B5-A11U 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11W         TCGA-B5-A11Y         TCGA-B5-A11Z 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A121         TCGA-BG-A0LW         TCGA-BG-A0LX 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0M0         TCGA-BG-A0M2         TCGA-BG-A0M3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0M4         TCGA-BG-A0M6         TCGA-BG-A0M7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0M8         TCGA-BG-A0M9         TCGA-BG-A0MC 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0MG         TCGA-BG-A0MS         TCGA-BG-A0MT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0MU         TCGA-BG-A0RY         TCGA-BG-A0VT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0VV         TCGA-BG-A0W1         TCGA-BG-A0YU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0YV         TCGA-BG-A186         TCGA-BG-A187 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A18A         TCGA-BG-A18B         TCGA-BG-A18C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BK-A0C9         TCGA-BK-A0CA         TCGA-BK-A0CB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BK-A0CC         TCGA-BK-A139         TCGA-BK-A13C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0T9         TCGA-BS-A0TA         TCGA-BS-A0TC 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0TD         TCGA-BS-A0TG         TCGA-BS-A0TI 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0TJ         TCGA-BS-A0U7         TCGA-BS-A0U8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0U9         TCGA-BS-A0UF         TCGA-BS-A0UJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0V7         TCGA-D1-A0ZP         TCGA-D1-A0ZR 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A0ZU         TCGA-D1-A0ZZ         TCGA-D1-A101 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A102         TCGA-D1-A103         TCGA-D1-A15V 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A15W         TCGA-D1-A15X         TCGA-D1-A15Z 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A160         TCGA-D1-A161         TCGA-D1-A163 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A165         TCGA-D1-A167         TCGA-D1-A168 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A169         TCGA-D1-A16B         TCGA-D1-A16D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A16E         TCGA-D1-A16G         TCGA-D1-A16I 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A16J         TCGA-D1-A16N         TCGA-D1-A16O 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A16Q         TCGA-D1-A16R         TCGA-D1-A16S 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A16V         TCGA-D1-A16X         TCGA-D1-A16Y 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A175         TCGA-D1-A176         TCGA-D1-A177 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A179         TCGA-D1-A17B         TCGA-D1-A17C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17D         TCGA-D1-A17F         TCGA-D1-A17H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17K         TCGA-D1-A17L         TCGA-D1-A17M 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17N         TCGA-D1-A17Q         TCGA-D1-A17R 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17S         TCGA-D1-A17T         TCGA-D1-A17U 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DI-A0WH 
"16Q GAIN WILD-TYPE" 
D28V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1    0
  16Q GAIN WILD-TYPE  120   73
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                120
  CLUS_2                0                 73
D28V7, multiclass
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                360 
        TCGA-A5-A0G1         TCGA-A5-A0G2         TCGA-A5-A0G5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0G9         TCGA-A5-A0GA         TCGA-A5-A0GB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GD         TCGA-A5-A0GE         TCGA-A5-A0GG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GH         TCGA-A5-A0GI         TCGA-A5-A0GJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GN         TCGA-A5-A0GP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GQ         TCGA-A5-A0GR         TCGA-A5-A0GU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GV         TCGA-A5-A0GW         TCGA-A5-A0GX 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0R6         TCGA-A5-A0R7         TCGA-A5-A0R8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0R9         TCGA-A5-A0RA         TCGA-A5-A0VP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0VQ         TCGA-A5-A1OF         TCGA-A5-A1OG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A1OJ         TCGA-A5-A1OK         TCGA-AJ-A23M 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AJ-A23O         TCGA-AJ-A2QK         TCGA-AJ-A2QL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AJ-A2QN         TCGA-AP-A051         TCGA-AP-A052 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A053         TCGA-AP-A054         TCGA-AP-A056 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A059         TCGA-AP-A05A         TCGA-AP-A05D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A05O         TCGA-AP-A05P         TCGA-AP-A0L8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LF         TCGA-AP-A0LG         TCGA-AP-A0LH 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LI         TCGA-AP-A0LJ         TCGA-AP-A0LL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LM         TCGA-AP-A0LN         TCGA-AP-A0LO 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LP         TCGA-AP-A0LS         TCGA-AP-A0LT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AP-A1DH         TCGA-AP-A1DK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A1DM         TCGA-AP-A1DO         TCGA-AP-A1DP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A1DQ         TCGA-AP-A1DR         TCGA-AP-A1DV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A1E0         TCGA-AP-A1E1         TCGA-AP-A1E3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A1E4         TCGA-AW-A1PO         TCGA-AX-A05S 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05Y 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A06D         TCGA-AX-A06F         TCGA-AX-A06H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A06L         TCGA-AX-A0IS 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A0IU         TCGA-AX-A0IW         TCGA-AX-A0IZ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A0J0         TCGA-AX-A0J1         TCGA-AX-A1C4 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A1C5         TCGA-AX-A1C7         TCGA-AX-A1C9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A1CA         TCGA-AX-A1CC         TCGA-AX-A1CE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A1CF         TCGA-AX-A1CI         TCGA-AX-A1CJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A1CK         TCGA-AX-A1CN         TCGA-AX-A1CP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A1CR         TCGA-AX-A2H2         TCGA-AX-A2H5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A2H7         TCGA-AX-A2H8         TCGA-AX-A2HA 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A2HC         TCGA-AX-A2HD         TCGA-AX-A2HF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A2HG         TCGA-AX-A2HJ         TCGA-AX-A2HK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A2IO         TCGA-B5-A0JS         TCGA-B5-A0JT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0JU         TCGA-B5-A0JV         TCGA-B5-A0JX 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0JY         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K2         TCGA-B5-A0K3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-B5-A0K6         TCGA-B5-A0K7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0K8         TCGA-B5-A0KB         TCGA-B5-A11E 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11F         TCGA-B5-A11G         TCGA-B5-A11H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11I         TCGA-B5-A11J         TCGA-B5-A11L 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11N         TCGA-B5-A11O         TCGA-B5-A11P 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11Q         TCGA-B5-A11S         TCGA-B5-A11U 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11W         TCGA-B5-A11Y         TCGA-B5-A11Z 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A121         TCGA-B5-A1MR         TCGA-B5-A1MU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A1MV         TCGA-B5-A1MX         TCGA-B5-A1MY 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A1MZ         TCGA-B5-A1N2         TCGA-BG-A0LW 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0LX         TCGA-BG-A0M0         TCGA-BG-A0M2 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0M3         TCGA-BG-A0M4         TCGA-BG-A0M6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0M7         TCGA-BG-A0M8         TCGA-BG-A0M9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0MA         TCGA-BG-A0MC         TCGA-BG-A0MG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BG-A0MO         TCGA-BG-A0MQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0MS         TCGA-BG-A0MT         TCGA-BG-A0MU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0RY         TCGA-BG-A0VT         TCGA-BG-A0VV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0VW         TCGA-BG-A0VX         TCGA-BG-A0VZ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0W1         TCGA-BG-A0W2         TCGA-BG-A0YU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0YV         TCGA-BG-A186         TCGA-BG-A187 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A18A         TCGA-BG-A18B         TCGA-BG-A18C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A220         TCGA-BG-A221         TCGA-BG-A222 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A2AD         TCGA-BG-A2AE         TCGA-BG-A2L7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BK-A0C9         TCGA-BK-A0CA         TCGA-BK-A0CB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BK-A0CC         TCGA-BK-A139         TCGA-BK-A13C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BK-A26L         TCGA-BS-A0T9         TCGA-BS-A0TA 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0TC         TCGA-BS-A0TD         TCGA-BS-A0TE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0TG         TCGA-BS-A0TI         TCGA-BS-A0TJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0U5         TCGA-BS-A0U7         TCGA-BS-A0U8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0U9         TCGA-BS-A0UA         TCGA-BS-A0UF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0UJ         TCGA-BS-A0UL         TCGA-BS-A0UT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0UV         TCGA-BS-A0V6         TCGA-BS-A0V8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0VI         TCGA-BS-A0WQ         TCGA-D1-A0ZN 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A0ZO         TCGA-D1-A0ZP         TCGA-D1-A0ZQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A0ZR         TCGA-D1-A0ZS         TCGA-D1-A0ZU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A0ZV         TCGA-D1-A0ZZ         TCGA-D1-A101 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A102         TCGA-D1-A103         TCGA-D1-A15V 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A15W         TCGA-D1-A15X         TCGA-D1-A15Z 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A160         TCGA-D1-A161         TCGA-D1-A163 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A165         TCGA-D1-A167         TCGA-D1-A168 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A169         TCGA-D1-A16B         TCGA-D1-A16D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A16E         TCGA-D1-A16G         TCGA-D1-A16I 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A16J         TCGA-D1-A16N         TCGA-D1-A16O 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A16Q         TCGA-D1-A16R         TCGA-D1-A16S 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A16V         TCGA-D1-A16X         TCGA-D1-A16Y 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A174         TCGA-D1-A175         TCGA-D1-A176 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A177         TCGA-D1-A179         TCGA-D1-A17A 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17B         TCGA-D1-A17C         TCGA-D1-A17D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17F         TCGA-D1-A17H         TCGA-D1-A17K 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17L         TCGA-D1-A17M         TCGA-D1-A17N 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17Q         TCGA-D1-A17R         TCGA-D1-A17S 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17T         TCGA-D1-A17U         TCGA-D1-A1NS 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A1NU         TCGA-D1-A1NW         TCGA-D1-A1NX 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A1NY         TCGA-D1-A1NZ         TCGA-D1-A1O0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A1O5         TCGA-D1-A1O7         TCGA-D1-A1O8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A2G5         TCGA-D1-A2G6         TCGA-D1-A2G7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DF-A2KS         TCGA-DI-A0WH         TCGA-DI-A1BY 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DI-A1NN         TCGA-DI-A1NO         TCGA-DI-A2QU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-E6-A1LX         TCGA-E6-A1LZ         TCGA-E6-A1M0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EC-A1NJ         TCGA-EC-A1QX         TCGA-EC-A24G 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EO-A1Y5         TCGA-EO-A1Y8         TCGA-EO-A22R 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EO-A22S         TCGA-EO-A22T         TCGA-EO-A2CG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EO-A2CH         TCGA-EY-A1G7         TCGA-EY-A1G8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A1GC         TCGA-EY-A1GD         TCGA-EY-A1GE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A1GF         TCGA-EY-A1GH         TCGA-EY-A1GI 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A1GK         TCGA-EY-A1GM         TCGA-EY-A1GQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A1GR         TCGA-EY-A1GS         TCGA-EY-A1GT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A1GU         TCGA-EY-A1GV         TCGA-EY-A1GW 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A1H0         TCGA-EY-A212         TCGA-EY-A214 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A215         TCGA-EY-A2OM         TCGA-FI-A2CX 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FI-A2CY         TCGA-FI-A2D0         TCGA-FI-A2D2 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FI-A2D4         TCGA-FI-A2D5         TCGA-FI-A2D6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FI-A2EU         TCGA-FI-A2EW         TCGA-FI-A2EX 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FI-A2F4         TCGA-FI-A2F8         TCGA-FI-A2F9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
D28V8, multiclass
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                360 
        TCGA-A5-A0G1         TCGA-A5-A0G2         TCGA-A5-A0G5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0G9         TCGA-A5-A0GA         TCGA-A5-A0GB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GD         TCGA-A5-A0GE         TCGA-A5-A0GG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GH         TCGA-A5-A0GI         TCGA-A5-A0GJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GN         TCGA-A5-A0GP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GQ         TCGA-A5-A0GR         TCGA-A5-A0GU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GV         TCGA-A5-A0GW         TCGA-A5-A0GX 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0R6         TCGA-A5-A0R7         TCGA-A5-A0R8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0R9         TCGA-A5-A0RA         TCGA-A5-A0VP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0VQ         TCGA-A5-A1OF         TCGA-A5-A1OG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A1OJ         TCGA-A5-A1OK         TCGA-AJ-A23M 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AJ-A23O         TCGA-AJ-A2QK         TCGA-AJ-A2QL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AJ-A2QN         TCGA-AP-A051         TCGA-AP-A052 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A053         TCGA-AP-A054         TCGA-AP-A056 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A059         TCGA-AP-A05A         TCGA-AP-A05D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A05O         TCGA-AP-A05P         TCGA-AP-A0L8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LF         TCGA-AP-A0LG         TCGA-AP-A0LH 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LI         TCGA-AP-A0LJ         TCGA-AP-A0LL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LM         TCGA-AP-A0LN         TCGA-AP-A0LO 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LP         TCGA-AP-A0LS         TCGA-AP-A0LT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AP-A1DH         TCGA-AP-A1DK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A1DM         TCGA-AP-A1DO         TCGA-AP-A1DP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A1DQ         TCGA-AP-A1DR         TCGA-AP-A1DV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A1E0         TCGA-AP-A1E1         TCGA-AP-A1E3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A1E4         TCGA-AW-A1PO         TCGA-AX-A05S 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05Y 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A06D         TCGA-AX-A06F         TCGA-AX-A06H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A06L         TCGA-AX-A0IS 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A0IU         TCGA-AX-A0IW         TCGA-AX-A0IZ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A0J0         TCGA-AX-A0J1         TCGA-AX-A1C4 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A1C5         TCGA-AX-A1C7         TCGA-AX-A1C9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A1CA         TCGA-AX-A1CC         TCGA-AX-A1CE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A1CF         TCGA-AX-A1CI         TCGA-AX-A1CJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A1CK         TCGA-AX-A1CN         TCGA-AX-A1CP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A1CR         TCGA-AX-A2H2         TCGA-AX-A2H5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A2H7         TCGA-AX-A2H8         TCGA-AX-A2HA 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A2HC         TCGA-AX-A2HD         TCGA-AX-A2HF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A2HG         TCGA-AX-A2HJ         TCGA-AX-A2HK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A2IO         TCGA-B5-A0JS         TCGA-B5-A0JT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0JU         TCGA-B5-A0JV         TCGA-B5-A0JX 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0JY         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K2         TCGA-B5-A0K3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-B5-A0K6         TCGA-B5-A0K7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0K8         TCGA-B5-A0KB         TCGA-B5-A11E 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11F         TCGA-B5-A11G         TCGA-B5-A11H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11I         TCGA-B5-A11J         TCGA-B5-A11L 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11N         TCGA-B5-A11O         TCGA-B5-A11P 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11Q         TCGA-B5-A11S         TCGA-B5-A11U 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11W         TCGA-B5-A11Y         TCGA-B5-A11Z 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A121         TCGA-B5-A1MR         TCGA-B5-A1MU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A1MV         TCGA-B5-A1MX         TCGA-B5-A1MY 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A1MZ         TCGA-B5-A1N2         TCGA-BG-A0LW 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0LX         TCGA-BG-A0M0         TCGA-BG-A0M2 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0M3         TCGA-BG-A0M4         TCGA-BG-A0M6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0M7         TCGA-BG-A0M8         TCGA-BG-A0M9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0MA         TCGA-BG-A0MC         TCGA-BG-A0MG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BG-A0MO         TCGA-BG-A0MQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0MS         TCGA-BG-A0MT         TCGA-BG-A0MU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0RY         TCGA-BG-A0VT         TCGA-BG-A0VV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0VW         TCGA-BG-A0VX         TCGA-BG-A0VZ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0W1         TCGA-BG-A0W2         TCGA-BG-A0YU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0YV         TCGA-BG-A186         TCGA-BG-A187 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A18A         TCGA-BG-A18B         TCGA-BG-A18C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A220         TCGA-BG-A221         TCGA-BG-A222 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A2AD         TCGA-BG-A2AE         TCGA-BG-A2L7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BK-A0C9         TCGA-BK-A0CA         TCGA-BK-A0CB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BK-A0CC         TCGA-BK-A139         TCGA-BK-A13C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BK-A26L         TCGA-BS-A0T9         TCGA-BS-A0TA 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0TC         TCGA-BS-A0TD         TCGA-BS-A0TE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0TG         TCGA-BS-A0TI         TCGA-BS-A0TJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0U5         TCGA-BS-A0U7         TCGA-BS-A0U8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0U9         TCGA-BS-A0UA         TCGA-BS-A0UF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0UJ         TCGA-BS-A0UL         TCGA-BS-A0UT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0UV         TCGA-BS-A0V6         TCGA-BS-A0V8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0VI         TCGA-BS-A0WQ         TCGA-D1-A0ZN 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A0ZO         TCGA-D1-A0ZP         TCGA-D1-A0ZQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A0ZR         TCGA-D1-A0ZS         TCGA-D1-A0ZU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A0ZV         TCGA-D1-A0ZZ         TCGA-D1-A101 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A102         TCGA-D1-A103         TCGA-D1-A15V 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A15W         TCGA-D1-A15X         TCGA-D1-A15Z 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A160         TCGA-D1-A161         TCGA-D1-A163 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A165         TCGA-D1-A167         TCGA-D1-A168 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A169         TCGA-D1-A16B         TCGA-D1-A16D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A16E         TCGA-D1-A16G         TCGA-D1-A16I 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A16J         TCGA-D1-A16N         TCGA-D1-A16O 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A16Q         TCGA-D1-A16R         TCGA-D1-A16S 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A16V         TCGA-D1-A16X         TCGA-D1-A16Y 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A174         TCGA-D1-A175         TCGA-D1-A176 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A177         TCGA-D1-A179         TCGA-D1-A17A 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17B         TCGA-D1-A17C         TCGA-D1-A17D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17F         TCGA-D1-A17H         TCGA-D1-A17K 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17L         TCGA-D1-A17M         TCGA-D1-A17N 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17Q         TCGA-D1-A17R         TCGA-D1-A17S 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17T         TCGA-D1-A17U         TCGA-D1-A1NS 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A1NU         TCGA-D1-A1NW         TCGA-D1-A1NX 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A1NY         TCGA-D1-A1NZ         TCGA-D1-A1O0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A1O5         TCGA-D1-A1O7         TCGA-D1-A1O8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A2G5         TCGA-D1-A2G6         TCGA-D1-A2G7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DF-A2KS         TCGA-DI-A0WH         TCGA-DI-A1BY 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DI-A1NN         TCGA-DI-A1NO         TCGA-DI-A2QU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-E6-A1LX         TCGA-E6-A1LZ         TCGA-E6-A1M0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EC-A1NJ         TCGA-EC-A1QX         TCGA-EC-A24G 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EO-A1Y5         TCGA-EO-A1Y8         TCGA-EO-A22R 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EO-A22S         TCGA-EO-A22T         TCGA-EO-A2CG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EO-A2CH         TCGA-EY-A1G7         TCGA-EY-A1G8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A1GC         TCGA-EY-A1GD         TCGA-EY-A1GE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A1GF         TCGA-EY-A1GH         TCGA-EY-A1GI 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A1GK         TCGA-EY-A1GM         TCGA-EY-A1GQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A1GR         TCGA-EY-A1GS         TCGA-EY-A1GT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A1GU         TCGA-EY-A1GV         TCGA-EY-A1GW 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A1H0         TCGA-EY-A212         TCGA-EY-A214 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A215         TCGA-EY-A2OM         TCGA-FI-A2CX 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FI-A2CY         TCGA-FI-A2D0         TCGA-FI-A2D2 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FI-A2D4         TCGA-FI-A2D5         TCGA-FI-A2D6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FI-A2EU         TCGA-FI-A2EW         TCGA-FI-A2EX 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FI-A2F4         TCGA-FI-A2F8         TCGA-FI-A2F9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
D28V9, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                192
  CLUS_2                1                145
  CLUS_3                1                138
D28V10, multiclass

Clustering(29) Variable = 17p gain mutation analysis
D29V1, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A0IW         TCGA-AX-A0J1         TCGA-B5-A0JR 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A0JZ         TCGA-B5-A0K0         TCGA-B5-A0K1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-BG-A0LW         TCGA-BG-A0MI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BK-A0C9 
"17P GAIN WILD-TYPE" 
D29V2, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A0IW         TCGA-AX-A0J1         TCGA-B5-A0JR 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A0JZ         TCGA-B5-A0K0         TCGA-B5-A0K1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-BG-A0LW         TCGA-BG-A0MI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BK-A0C9 
"17P GAIN WILD-TYPE" 
D29V3, multiclass
D29V4, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                4                139
  CLUS_2                0                 85
  CLUS_3                1                148
D29V5, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                192 
        TCGA-A5-A0G1         TCGA-A5-A0G2         TCGA-A5-A0G5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0G9         TCGA-A5-A0GA         TCGA-A5-A0GB 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GD         TCGA-A5-A0GE         TCGA-A5-A0GG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GH         TCGA-A5-A0GI         TCGA-A5-A0GJ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GN         TCGA-A5-A0GQ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GR         TCGA-A5-A0GU         TCGA-A5-A0GV 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GW         TCGA-A5-A0GX         TCGA-A5-A0R6 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0R7         TCGA-A5-A0R8         TCGA-A5-A0R9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0RA         TCGA-A5-A0VP         TCGA-A5-A0VQ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A059 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A05A         TCGA-AP-A05D         TCGA-AP-A05H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05O 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0LD         TCGA-AP-A0LE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0LF         TCGA-AP-A0LG         TCGA-AP-A0LH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0LI         TCGA-AP-A0LJ         TCGA-AP-A0LL 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0LM         TCGA-AP-A0LN         TCGA-AP-A0LP 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06D         TCGA-AX-A06F 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A06L         TCGA-AX-A0IS 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A0IW         TCGA-AX-A0IZ         TCGA-AX-A0J0 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JN         TCGA-B5-A0JT 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A0JY         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K2         TCGA-B5-A0K3 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-B5-A0K7         TCGA-B5-A0K9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A11E         TCGA-B5-A11F         TCGA-B5-A11G 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A11H         TCGA-B5-A11I         TCGA-B5-A11N 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A11Q         TCGA-B5-A11S         TCGA-B5-A11U 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A11V         TCGA-B5-A11W         TCGA-B5-A11Y 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A11Z         TCGA-B5-A121         TCGA-BG-A0LW 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BG-A0LX         TCGA-BG-A0M0         TCGA-BG-A0M2 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BG-A0M3         TCGA-BG-A0M6         TCGA-BG-A0M7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BG-A0M8         TCGA-BG-A0M9         TCGA-BG-A0MC 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BG-A0MG         TCGA-BG-A0MS         TCGA-BG-A0MT 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BG-A0MU         TCGA-BG-A0RY         TCGA-BG-A0VT 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BG-A0VV         TCGA-BG-A0W1         TCGA-BG-A0YU 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BG-A0YV         TCGA-BG-A186         TCGA-BG-A187 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BG-A18A         TCGA-BG-A18B         TCGA-BG-A18C 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BK-A0C9         TCGA-BK-A0CA         TCGA-BK-A0CB 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BK-A139         TCGA-BK-A13C         TCGA-BS-A0T9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BS-A0TA         TCGA-BS-A0TC         TCGA-BS-A0TD 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BS-A0TG         TCGA-BS-A0TI         TCGA-BS-A0TJ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BS-A0U7         TCGA-BS-A0U8         TCGA-BS-A0U9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BS-A0UF         TCGA-BS-A0UJ         TCGA-BS-A0V7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A0ZP         TCGA-D1-A0ZR         TCGA-D1-A0ZU 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A0ZZ         TCGA-D1-A101         TCGA-D1-A102 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A103         TCGA-D1-A15V         TCGA-D1-A15W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A15X         TCGA-D1-A15Z         TCGA-D1-A160 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A161         TCGA-D1-A163         TCGA-D1-A165 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A167         TCGA-D1-A168         TCGA-D1-A169 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A16B         TCGA-D1-A16D         TCGA-D1-A16E 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A16G         TCGA-D1-A16I         TCGA-D1-A16J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A16N         TCGA-D1-A16O         TCGA-D1-A16Q 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A16R         TCGA-D1-A16S         TCGA-D1-A16V 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A16X         TCGA-D1-A16Y         TCGA-D1-A175 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A176         TCGA-D1-A177         TCGA-D1-A179 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A17B         TCGA-D1-A17C         TCGA-D1-A17D 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A17F         TCGA-D1-A17H         TCGA-D1-A17K 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A17L         TCGA-D1-A17M         TCGA-D1-A17N 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A17Q         TCGA-D1-A17R         TCGA-D1-A17S 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A17T         TCGA-D1-A17U         TCGA-DI-A0WH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D29V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1    1
  17P GAIN WILD-TYPE  120   72
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                1                120
  CLUS_2                1                 72
D29V7, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                3                139
  CLUS_2                1                106
  CLUS_3                0                113
D29V8, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                0                 65
  CLUS_2                0                 92
  CLUS_3                2                 63
  CLUS_4                2                138
D29V9, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                4                190
  CLUS_2                0                146
  CLUS_3                3                136
D29V10, multiclass

Clustering(30) Variable = 17q gain mutation analysis
D30V1, multiclass
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A0IW         TCGA-AX-A0J1         TCGA-B5-A0JR 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B5-A0JZ         TCGA-B5-A0K0         TCGA-B5-A0K1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-BG-A0LW         TCGA-BG-A0MI 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BK-A0C9 
"17Q GAIN WILD-TYPE" 
D30V2, multiclass
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A0IW         TCGA-AX-A0J1         TCGA-B5-A0JR 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B5-A0JZ         TCGA-B5-A0K0         TCGA-B5-A0K1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-BG-A0LW         TCGA-BG-A0MI 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BK-A0C9 
"17Q GAIN WILD-TYPE" 
D30V3, multiclass
D30V4, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                9                134
  CLUS_2                0                 85
  CLUS_3                1                148
D30V5, multiclass
D30V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3    1
  17Q GAIN WILD-TYPE  118   72
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                3                118
  CLUS_2                1                 72
D30V7, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                7                135
  CLUS_2                2                105
  CLUS_3                0                113
D30V8, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                0                 65
  CLUS_2                1                 91
  CLUS_3                2                 63
  CLUS_4                6                134
D30V9, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                9                185
  CLUS_2                1                145
  CLUS_3                3                136
D30V10, multiclass

Clustering(31) Variable = 18p gain mutation analysis
D31V1, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                4                 14
  CLUS_3                0                 14
  CLUS_4                0                  8
D31V2, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                 20
  CLUS_2                1                 14
  CLUS_3                3                 15
D31V3, multiclass
D31V4, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               20                123
  CLUS_2                8                 77
  CLUS_3                2                147
D31V5, multiclass
D31V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3    4
  18P GAIN WILD-TYPE  118   69
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                3                118
  CLUS_2                4                 69
D31V7, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               18                124
  CLUS_2                2                105
  CLUS_3                1                112
D31V8, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                 65
  CLUS_2                1                 91
  CLUS_3                0                 65
  CLUS_4               20                120
D31V9, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               33                161
  CLUS_2                1                145
  CLUS_3                2                137
D31V10, multiclass

Clustering(32) Variable = 18q gain mutation analysis
D32V1, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                3                 15
  CLUS_3                0                 14
  CLUS_4                0                  8
D32V2, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                 20
  CLUS_2                0                 15
  CLUS_3                3                 15
D32V3, multiclass
D32V4, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                8                135
  CLUS_2                7                 78
  CLUS_3                1                148
D32V5, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                192 
        TCGA-A5-A0G1         TCGA-A5-A0G2         TCGA-A5-A0G5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A5-A0G9         TCGA-A5-A0GA         TCGA-A5-A0GB 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A5-A0GD         TCGA-A5-A0GE         TCGA-A5-A0GG 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A5-A0GH         TCGA-A5-A0GI         TCGA-A5-A0GJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GN         TCGA-A5-A0GQ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A5-A0GR         TCGA-A5-A0GU         TCGA-A5-A0GV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A5-A0GW         TCGA-A5-A0GX         TCGA-A5-A0R6 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A5-A0R7         TCGA-A5-A0R8         TCGA-A5-A0R9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A5-A0RA         TCGA-A5-A0VP         TCGA-A5-A0VQ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A054 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A059         TCGA-AP-A05A 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05O         TCGA-AP-A05P 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LE         TCGA-AP-A0LF 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LI 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LL         TCGA-AP-A0LM 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LP         TCGA-AP-A0LT 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AX-A06D         TCGA-AX-A06F         TCGA-AX-A06J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AX-A06L         TCGA-AX-A0IS         TCGA-AX-A0IW 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AX-A0IZ         TCGA-AX-A0J0         TCGA-AX-A0J1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B5-A0JN         TCGA-B5-A0JT         TCGA-B5-A0JY 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B5-A0JZ         TCGA-B5-A0K0         TCGA-B5-A0K1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B5-A0K2         TCGA-B5-A0K3         TCGA-B5-A0K4 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B5-A0K7         TCGA-B5-A0K9         TCGA-B5-A11E 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B5-A11F         TCGA-B5-A11G         TCGA-B5-A11H 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B5-A11I         TCGA-B5-A11N         TCGA-B5-A11Q 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B5-A11S         TCGA-B5-A11U         TCGA-B5-A11V 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B5-A11W         TCGA-B5-A11Y         TCGA-B5-A11Z 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B5-A121         TCGA-BG-A0LW         TCGA-BG-A0LX 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BG-A0M0         TCGA-BG-A0M2         TCGA-BG-A0M3 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BG-A0M4         TCGA-BG-A0M6         TCGA-BG-A0M7 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BG-A0M8         TCGA-BG-A0M9         TCGA-BG-A0MC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BG-A0MG         TCGA-BG-A0MS         TCGA-BG-A0MT 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BG-A0MU         TCGA-BG-A0RY         TCGA-BG-A0VT 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BG-A0VV         TCGA-BG-A0W1         TCGA-BG-A0YU 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BG-A0YV         TCGA-BG-A186         TCGA-BG-A187 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BG-A18A         TCGA-BG-A18B         TCGA-BG-A18C 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BK-A0C9         TCGA-BK-A0CA         TCGA-BK-A0CB 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BK-A0CC         TCGA-BK-A139         TCGA-BK-A13C 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BS-A0T9         TCGA-BS-A0TA         TCGA-BS-A0TC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BS-A0TD         TCGA-BS-A0TG         TCGA-BS-A0TI 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BS-A0TJ         TCGA-BS-A0U7         TCGA-BS-A0U8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BS-A0U9         TCGA-BS-A0UF         TCGA-BS-A0UJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BS-A0V7         TCGA-D1-A0ZP         TCGA-D1-A0ZR 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A0ZU         TCGA-D1-A0ZZ         TCGA-D1-A101 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A102         TCGA-D1-A103         TCGA-D1-A15V 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A15W         TCGA-D1-A15X         TCGA-D1-A15Z 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A160         TCGA-D1-A161         TCGA-D1-A163 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A165         TCGA-D1-A167         TCGA-D1-A168 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A169         TCGA-D1-A16B         TCGA-D1-A16D 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A16E         TCGA-D1-A16G         TCGA-D1-A16J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A16N         TCGA-D1-A16O         TCGA-D1-A16Q 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A16R         TCGA-D1-A16S         TCGA-D1-A16V 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A16X         TCGA-D1-A16Y         TCGA-D1-A175 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A176         TCGA-D1-A177         TCGA-D1-A179 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A17B         TCGA-D1-A17C         TCGA-D1-A17D 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A17F         TCGA-D1-A17H         TCGA-D1-A17K 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A17L         TCGA-D1-A17M         TCGA-D1-A17N 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A17Q         TCGA-D1-A17R         TCGA-D1-A17S 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A17T         TCGA-D1-A17U         TCGA-DI-A0WH 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
D32V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    1
  18Q GAIN WILD-TYPE  120   72
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                120
  CLUS_2                1                 72
D32V7, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                9                133
  CLUS_2                1                106
  CLUS_3                1                112
D32V8, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                 65
  CLUS_2                1                 91
  CLUS_3                0                 65
  CLUS_4               10                130
D32V9, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               17                177
  CLUS_2                0                146
  CLUS_3                2                137
D32V10, multiclass

Clustering(33) Variable = 19p gain mutation analysis
D33V1, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                4                 14
  CLUS_3                0                 14
  CLUS_4                0                  8
D33V2, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                 20
  CLUS_2                0                 15
  CLUS_3                4                 14
D33V3, multiclass
D33V4, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               16                127
  CLUS_2                7                 78
  CLUS_3                3                146
D33V5, multiclass
D33V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1    3
  19P GAIN WILD-TYPE  120   70
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                120
  CLUS_2                3                 70
D33V7, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               16                126
  CLUS_2                1                106
  CLUS_3                0                113
D33V8, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                 65
  CLUS_2                0                 92
  CLUS_3                1                 64
  CLUS_4               16                124
D33V9, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               25                169
  CLUS_2                3                143
  CLUS_3                3                136
D33V10, multiclass

Clustering(34) Variable = 19q gain mutation analysis
D34V1, multiclass
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0J1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
D34V2, multiclass
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0J1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
D34V3, multiclass
D34V4, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               15                128
  CLUS_2                7                 78
  CLUS_3                2                147
D34V5, multiclass
D34V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2    1
  19Q GAIN WILD-TYPE  119   72
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                119
  CLUS_2                1                 72
D34V7, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               16                126
  CLUS_2                1                106
  CLUS_3                0                113
D34V8, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                 65
  CLUS_2                0                 92
  CLUS_3                0                 65
  CLUS_4               17                123
D34V9, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               24                170
  CLUS_2                2                144
  CLUS_3                2                137
D34V10, multiclass

Clustering(35) Variable = 20p gain mutation analysis
D35V1, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                3                 15
  CLUS_3                0                 14
  CLUS_4                0                  8
D35V2, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                0                 20
  CLUS_2                0                 15
  CLUS_3                3                 15
D35V3, multiclass
D35V4, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               37                106
  CLUS_2                9                 76
  CLUS_3               11                138
D35V5, multiclass
D35V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      8    5
  20P GAIN WILD-TYPE  113   68
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                8                113
  CLUS_2                5                 68
D35V7, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               27                115
  CLUS_2                5                102
  CLUS_3                5                108
D35V8, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                4                 61
  CLUS_2                5                 87
  CLUS_3                4                 61
  CLUS_4               24                116
D35V9, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               48                146
  CLUS_2                8                138
  CLUS_3                9                130
D35V10, multiclass

Clustering(36) Variable = 20q gain mutation analysis
D36V1, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                4                 14
  CLUS_3                0                 14
  CLUS_4                0                  8
D36V2, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                0                 20
  CLUS_2                0                 15
  CLUS_3                4                 14
D36V3, multiclass
D36V4, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               47                 96
  CLUS_2               10                 75
  CLUS_3               12                137
D36V5, multiclass
D36V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      8    7
  20Q GAIN WILD-TYPE  113   66
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                8                113
  CLUS_2                7                 66
D36V7, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               32                110
  CLUS_2                5                102
  CLUS_3                5                108
D36V8, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                4                 61
  CLUS_2                5                 87
  CLUS_3                4                 61
  CLUS_4               29                111
D36V9, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               59                135
  CLUS_2                9                137
  CLUS_3                9                130
D36V10, multiclass

Clustering(37) Variable = 21q gain mutation analysis
D37V1, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0GA         TCGA-A5-A0GB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0J1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D37V2, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0GA         TCGA-A5-A0GB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0J1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D37V3, multiclass
D37V4, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               12                131
  CLUS_2                6                 79
  CLUS_3                4                145
D37V5, multiclass
D37V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1    2
  21Q GAIN WILD-TYPE  120   71
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                120
  CLUS_2                2                 71
D37V7, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               12                130
  CLUS_2                1                106
  CLUS_3                0                113
D37V8, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                 65
  CLUS_2                1                 91
  CLUS_3                1                 64
  CLUS_4               11                129
D37V9, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               20                174
  CLUS_2                4                142
  CLUS_3                1                138
D37V10, multiclass

Clustering(38) Variable = 22q gain mutation analysis
D38V1, multiclass
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0GA         TCGA-A5-A0GB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0IW 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BK-A0CC 
"22Q GAIN WILD-TYPE" 
D38V2, multiclass
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0GA         TCGA-A5-A0GB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0IW 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BK-A0CC 
"22Q GAIN WILD-TYPE" 
D38V3, multiclass
D38V4, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                8                135
  CLUS_2                0                 85
  CLUS_3                0                149
D38V5, multiclass
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                193 
        TCGA-A5-A0G1         TCGA-A5-A0G2         TCGA-A5-A0G9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GA         TCGA-A5-A0GB         TCGA-A5-A0GD 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GG         TCGA-A5-A0GH 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GI         TCGA-A5-A0GJ         TCGA-A5-A0GM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GN         TCGA-A5-A0GQ         TCGA-A5-A0GR 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GU         TCGA-A5-A0GV         TCGA-A5-A0GW 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GX         TCGA-A5-A0R6         TCGA-A5-A0R7 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0R8         TCGA-A5-A0R9         TCGA-A5-A0RA 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0VP         TCGA-A5-A0VQ         TCGA-AP-A051 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A059         TCGA-AP-A05A 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05O         TCGA-AP-A05P 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LE         TCGA-AP-A0LF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LI 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LL         TCGA-AP-A0LM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LP         TCGA-AP-A0LT 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A06D         TCGA-AX-A06F         TCGA-AX-A06J 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A06L         TCGA-AX-A0IS         TCGA-AX-A0IW 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A0IZ         TCGA-AX-A0J0         TCGA-AX-A0J1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A0JN         TCGA-B5-A0JT         TCGA-B5-A0JY 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A0JZ         TCGA-B5-A0K0         TCGA-B5-A0K1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A0K2         TCGA-B5-A0K3         TCGA-B5-A0K4 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A0K7         TCGA-B5-A0K9         TCGA-B5-A11E 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A11F         TCGA-B5-A11G         TCGA-B5-A11H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A11I         TCGA-B5-A11N         TCGA-B5-A11Q 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A11S         TCGA-B5-A11U         TCGA-B5-A11V 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A11W         TCGA-B5-A11Y         TCGA-B5-A11Z 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A121         TCGA-BG-A0LW         TCGA-BG-A0LX 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BG-A0M0         TCGA-BG-A0M2         TCGA-BG-A0M3 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BG-A0M4         TCGA-BG-A0M6         TCGA-BG-A0M7 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BG-A0M8         TCGA-BG-A0M9         TCGA-BG-A0MC 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BG-A0MG         TCGA-BG-A0MS         TCGA-BG-A0MT 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BG-A0MU         TCGA-BG-A0RY         TCGA-BG-A0VT 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BG-A0VV         TCGA-BG-A0W1         TCGA-BG-A0YU 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BG-A0YV         TCGA-BG-A186         TCGA-BG-A187 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BG-A18A         TCGA-BG-A18B         TCGA-BG-A18C 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BK-A0C9         TCGA-BK-A0CA         TCGA-BK-A0CB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BK-A0CC         TCGA-BK-A139         TCGA-BK-A13C 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BS-A0T9         TCGA-BS-A0TA         TCGA-BS-A0TC 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BS-A0TD         TCGA-BS-A0TG         TCGA-BS-A0TI 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BS-A0TJ         TCGA-BS-A0U7         TCGA-BS-A0U8 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BS-A0U9         TCGA-BS-A0UF         TCGA-BS-A0UJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BS-A0V7         TCGA-D1-A0ZP         TCGA-D1-A0ZR 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A0ZU         TCGA-D1-A0ZZ         TCGA-D1-A101 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A102         TCGA-D1-A103         TCGA-D1-A15V 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A15W         TCGA-D1-A15X         TCGA-D1-A15Z 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A160         TCGA-D1-A161         TCGA-D1-A163 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A165         TCGA-D1-A167         TCGA-D1-A168 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A169         TCGA-D1-A16B         TCGA-D1-A16D 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A16E         TCGA-D1-A16G         TCGA-D1-A16I 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A16J         TCGA-D1-A16N         TCGA-D1-A16O 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A16Q         TCGA-D1-A16R         TCGA-D1-A16S 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A16V         TCGA-D1-A16X         TCGA-D1-A16Y 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A175         TCGA-D1-A176         TCGA-D1-A177 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A179         TCGA-D1-A17B         TCGA-D1-A17C 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A17D         TCGA-D1-A17F         TCGA-D1-A17H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A17K         TCGA-D1-A17L         TCGA-D1-A17M 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A17N         TCGA-D1-A17Q         TCGA-D1-A17R 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A17S         TCGA-D1-A17T         TCGA-D1-A17U 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DI-A0WH 
"22Q GAIN WILD-TYPE" 
D38V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0    1
  22Q GAIN WILD-TYPE  121   72
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                0                121
  CLUS_2                1                 72
D38V7, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                3                139
  CLUS_2                0                107
  CLUS_3                0                113
D38V8, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                0                 65
  CLUS_2                0                 92
  CLUS_3                0                 65
  CLUS_4                3                137
D38V9, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                9                185
  CLUS_2                0                146
  CLUS_3                0                139
D38V10, multiclass

Clustering(39) Variable = Xq gain mutation analysis
D39V1, multiclass
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D39V2, multiclass
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D39V3, multiclass
D39V4, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               6               137
  CLUS_2               2                83
  CLUS_3               2               147
D39V5, multiclass
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1               193 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0G9 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A5-A0GG        TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A5-A0GM        TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A5-A0R6        TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A5-A0RA        TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A059        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A0LM        TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A06D        TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A0IS        TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A0J1        TCGA-B5-A0JN        TCGA-B5-A0JT        TCGA-B5-A0JY 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K2 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B5-A0K3        TCGA-B5-A0K4        TCGA-B5-A0K7        TCGA-B5-A0K9 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B5-A11E        TCGA-B5-A11F        TCGA-B5-A11G        TCGA-B5-A11H 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B5-A11I        TCGA-B5-A11N        TCGA-B5-A11Q        TCGA-B5-A11S 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B5-A11U        TCGA-B5-A11V        TCGA-B5-A11W        TCGA-B5-A11Y 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B5-A11Z        TCGA-B5-A121        TCGA-BG-A0LW        TCGA-BG-A0LX 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BG-A0M0        TCGA-BG-A0M2        TCGA-BG-A0M3        TCGA-BG-A0M4 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BG-A0M7        TCGA-BG-A0M8        TCGA-BG-A0M9        TCGA-BG-A0MC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BG-A0MG        TCGA-BG-A0MS        TCGA-BG-A0MT        TCGA-BG-A0MU 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BG-A0RY        TCGA-BG-A0VT        TCGA-BG-A0VV        TCGA-BG-A0W1 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BG-A0YU        TCGA-BG-A0YV        TCGA-BG-A186        TCGA-BG-A187 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BG-A18A        TCGA-BG-A18B        TCGA-BG-A18C        TCGA-BK-A0C9 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BK-A0CA        TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BK-A13C        TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BS-A0TD        TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BS-A0U7        TCGA-BS-A0U8        TCGA-BS-A0U9        TCGA-BS-A0UF 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BS-A0UJ        TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D1-A0ZU        TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D1-A103        TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D1-A15Z        TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D1-A165        TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D1-A16B        TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D1-A16I        TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D1-A16Q        TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D1-A16X        TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D1-A177        TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D1-A17D        TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D1-A17L        TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D1-A17R        TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DI-A0WH 
"XQ GAIN WILD-TYPE" 
D39V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0    1
  XQ GAIN WILD-TYPE  121   72
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0               121
  CLUS_2               1                72
D39V7, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               4               138
  CLUS_2               1               106
  CLUS_3               0               113
D39V8, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                65
  CLUS_2               1                91
  CLUS_3               0                65
  CLUS_4               4               136
D39V9, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              10               184
  CLUS_2               2               144
  CLUS_3               0               139
D39V10, multiclass

Clustering(40) Variable = 1p loss mutation analysis
D40V1, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                51 
       TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP        TCGA-A5-A0GU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH        TCGA-AP-A0LJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV        TCGA-AX-A05S 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W        TCGA-AX-A05Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062        TCGA-AX-A063 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F        TCGA-AX-A06J 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR        TCGA-B5-A0JZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4        TCGA-BG-A0LW 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D40V2, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                51 
       TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP        TCGA-A5-A0GU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH        TCGA-AP-A0LJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV        TCGA-AX-A05S 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W        TCGA-AX-A05Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062        TCGA-AX-A063 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F        TCGA-AX-A06J 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR        TCGA-B5-A0JZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4        TCGA-BG-A0LW 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D40V3, multiclass
D40V4, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               9               134
  CLUS_2               1                84
  CLUS_3               0               149
D40V5, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G5        TCGA-A5-A0G9        TCGA-A5-A0GA 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE        TCGA-A5-A0GG 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ        TCGA-A5-A0GM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A5-A0GQ        TCGA-A5-A0GR        TCGA-A5-A0GU        TCGA-A5-A0GV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A5-A0GW        TCGA-A5-A0GX        TCGA-A5-A0R6        TCGA-A5-A0R7 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A5-A0R8        TCGA-A5-A0R9        TCGA-A5-A0RA        TCGA-A5-A0VP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A5-A0VQ        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A059        TCGA-AP-A05A 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A05D        TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A05O        TCGA-AP-A05P        TCGA-AP-A0LD        TCGA-AP-A0LE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A0LF        TCGA-AP-A0LG        TCGA-AP-A0LH        TCGA-AP-A0LI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LL        TCGA-AP-A0LM        TCGA-AP-A0LN 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A0LP        TCGA-AP-A0LT        TCGA-AP-A0LV        TCGA-AX-A05S 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W        TCGA-AX-A05Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062        TCGA-AX-A063 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06D        TCGA-AX-A06F 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A06L        TCGA-AX-A0IS        TCGA-AX-A0IW 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A0IZ        TCGA-AX-A0J0        TCGA-AX-A0J1        TCGA-B5-A0JN 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B5-A0JT        TCGA-B5-A0JY        TCGA-B5-A0JZ        TCGA-B5-A0K0 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B5-A0K1        TCGA-B5-A0K2        TCGA-B5-A0K3        TCGA-B5-A0K4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B5-A0K7        TCGA-B5-A0K9        TCGA-B5-A11E        TCGA-B5-A11F 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B5-A11G        TCGA-B5-A11H        TCGA-B5-A11I        TCGA-B5-A11N 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B5-A11Q        TCGA-B5-A11S        TCGA-B5-A11U        TCGA-B5-A11V 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B5-A11W        TCGA-B5-A11Y        TCGA-B5-A11Z        TCGA-B5-A121 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0LX        TCGA-BG-A0M0        TCGA-BG-A0M2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BG-A0M3        TCGA-BG-A0M4        TCGA-BG-A0M6        TCGA-BG-A0M7 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BG-A0M8        TCGA-BG-A0M9        TCGA-BG-A0MC        TCGA-BG-A0MG 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BG-A0MS        TCGA-BG-A0MT        TCGA-BG-A0MU        TCGA-BG-A0RY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BG-A0VT        TCGA-BG-A0VV        TCGA-BG-A0W1        TCGA-BG-A0YU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BG-A0YV        TCGA-BG-A186        TCGA-BG-A187        TCGA-BG-A18A 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BG-A18B        TCGA-BG-A18C        TCGA-BK-A0C9        TCGA-BK-A0CA 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139        TCGA-BK-A13C 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC        TCGA-BS-A0TD 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ        TCGA-BS-A0U7 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BS-A0U8        TCGA-BS-A0U9        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D40V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    1
  1P LOSS WILD-TYPE  120   72
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1               120
  CLUS_2               1                72
D40V7, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               6               136
  CLUS_2               0               107
  CLUS_3               1               112
D40V8, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                64
  CLUS_2               0                92
  CLUS_3               0                65
  CLUS_4               6               134
D40V9, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              10               184
  CLUS_2               1               145
  CLUS_3               1               138
D40V10, multiclass

Clustering(41) Variable = 1q loss mutation analysis
D41V1, multiclass
D41V2, multiclass
D41V3, multiclass
D41V4, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               4               139
  CLUS_2               0                85
  CLUS_3               0               149
D41V5, multiclass
D41V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0    0
  1Q LOSS WILD-TYPE  121   73
D41V7, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               3               139
  CLUS_2               0               107
  CLUS_3               0               113
D41V8, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               0                65
  CLUS_2               0                92
  CLUS_3               0                65
  CLUS_4               3               137
D41V9, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               4               190
  CLUS_2               0               146
  CLUS_3               0               139
D41V10, multiclass

Clustering(42) Variable = 2p loss mutation analysis
D42V1, multiclass
D42V2, multiclass
D42V3, multiclass
D42V4, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               3               140
  CLUS_2               2                83
  CLUS_3               1               148
D42V5, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0G9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0GG        TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0GM        TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0R6        TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0RA        TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A059        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A0LM        TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AX-A06D        TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AX-A0IS        TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AX-A0J1        TCGA-B5-A0JN        TCGA-B5-A0JT        TCGA-B5-A0JY 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K2 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A0K3        TCGA-B5-A0K4        TCGA-B5-A0K7        TCGA-B5-A0K9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A11E        TCGA-B5-A11F        TCGA-B5-A11G        TCGA-B5-A11H 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A11I        TCGA-B5-A11N        TCGA-B5-A11Q        TCGA-B5-A11S 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A11U        TCGA-B5-A11V        TCGA-B5-A11W        TCGA-B5-A11Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A11Z        TCGA-B5-A121        TCGA-BG-A0LW        TCGA-BG-A0LX 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A0M0        TCGA-BG-A0M2        TCGA-BG-A0M3        TCGA-BG-A0M4 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A0M6        TCGA-BG-A0M7        TCGA-BG-A0M8        TCGA-BG-A0M9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A0MC        TCGA-BG-A0MG        TCGA-BG-A0MS        TCGA-BG-A0MT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A0MU        TCGA-BG-A0RY        TCGA-BG-A0VT        TCGA-BG-A0VV 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A0W1        TCGA-BG-A0YU        TCGA-BG-A0YV        TCGA-BG-A186 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A187        TCGA-BG-A18A        TCGA-BG-A18B        TCGA-BK-A0C9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BK-A0CA        TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BK-A13C        TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BS-A0TD        TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BS-A0U7        TCGA-BS-A0U8        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D42V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0    2
  2P LOSS WILD-TYPE  121   71
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0               121
  CLUS_2               2                71
D42V7, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               4               138
  CLUS_2               1               106
  CLUS_3               0               113
D42V8, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0                65
  CLUS_2               0                92
  CLUS_3               0                65
  CLUS_4               5               135
D42V9, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               3               191
  CLUS_2               1               145
  CLUS_3               2               137
D42V10, multiclass

Clustering(43) Variable = 2q loss mutation analysis
D43V1, multiclass
D43V2, multiclass
D43V3, multiclass
D43V4, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               4               139
  CLUS_2               3                82
  CLUS_3               1               148
D43V5, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0G9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GG        TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GM        TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0R6        TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0RA        TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A059        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0LM        TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A06D        TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A0IS        TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A0J1        TCGA-B5-A0JN        TCGA-B5-A0JT        TCGA-B5-A0JY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K2 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A0K3        TCGA-B5-A0K4        TCGA-B5-A0K7        TCGA-B5-A0K9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A11E        TCGA-B5-A11F        TCGA-B5-A11G        TCGA-B5-A11H 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A11I        TCGA-B5-A11N        TCGA-B5-A11Q        TCGA-B5-A11S 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A11U        TCGA-B5-A11V        TCGA-B5-A11W        TCGA-B5-A11Y 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A11Z        TCGA-B5-A121        TCGA-BG-A0LW        TCGA-BG-A0LX 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0M0        TCGA-BG-A0M2        TCGA-BG-A0M3        TCGA-BG-A0M4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0M6        TCGA-BG-A0M7        TCGA-BG-A0M8        TCGA-BG-A0M9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0MC        TCGA-BG-A0MG        TCGA-BG-A0MS        TCGA-BG-A0MT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0MU        TCGA-BG-A0RY        TCGA-BG-A0VT        TCGA-BG-A0VV 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0W1        TCGA-BG-A0YU        TCGA-BG-A0YV        TCGA-BG-A186 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A187        TCGA-BG-A18A        TCGA-BG-A18B        TCGA-BK-A0C9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BK-A0CA        TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BK-A13C        TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BS-A0TD        TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BS-A0U7        TCGA-BS-A0U8        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D43V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0    2
  2Q LOSS WILD-TYPE  121   71
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0               121
  CLUS_2               2                71
D43V7, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               4               138
  CLUS_2               1               106
  CLUS_3               0               113
D43V8, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0                65
  CLUS_2               0                92
  CLUS_3               0                65
  CLUS_4               5               135
D43V9, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               5               189
  CLUS_2               1               145
  CLUS_3               2               137
D43V10, multiclass

Clustering(44) Variable = 3p loss mutation analysis
D44V1, multiclass
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2                51 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A053        TCGA-AP-A054 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05H        TCGA-AP-A05J 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8        TCGA-AP-A0L9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH        TCGA-AP-A0LJ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV        TCGA-AX-A05S 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W        TCGA-AX-A05Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062        TCGA-AX-A063 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F        TCGA-AX-A06J 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR        TCGA-B5-A0JZ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4        TCGA-BG-A0LW 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
D44V2, multiclass
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2                51 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A053        TCGA-AP-A054 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05H        TCGA-AP-A05J 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8        TCGA-AP-A0L9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH        TCGA-AP-A0LJ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV        TCGA-AX-A05S 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W        TCGA-AX-A05Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062        TCGA-AX-A063 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F        TCGA-AX-A06J 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR        TCGA-B5-A0JZ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4        TCGA-BG-A0LW 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
D44V3, multiclass
D44V4, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              19               124
  CLUS_2               6                79
  CLUS_3               2               147
D44V5, multiclass
D44V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2    7
  3P LOSS WILD-TYPE  119   66
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               2               119
  CLUS_2               7                66
D44V7, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              19               123
  CLUS_2               1               106
  CLUS_3               0               113
D44V8, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                65
  CLUS_2               0                92
  CLUS_3               0                65
  CLUS_4              20               120
D44V9, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              23               171
  CLUS_2               2               144
  CLUS_3               4               135
D44V10, multiclass

Clustering(45) Variable = 3q loss mutation analysis
D45V1, multiclass
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                51 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A053        TCGA-AP-A054 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05H        TCGA-AP-A05J 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8        TCGA-AP-A0L9 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH        TCGA-AP-A0LJ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV        TCGA-AX-A05S 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W        TCGA-AX-A05Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062        TCGA-AX-A063 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F        TCGA-AX-A06J 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR        TCGA-B5-A0JZ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4        TCGA-BG-A0LW 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
D45V2, multiclass
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                51 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A053        TCGA-AP-A054 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05H        TCGA-AP-A05J 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8        TCGA-AP-A0L9 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH        TCGA-AP-A0LJ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV        TCGA-AX-A05S 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W        TCGA-AX-A05Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062        TCGA-AX-A063 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F        TCGA-AX-A06J 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR        TCGA-B5-A0JZ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4        TCGA-BG-A0LW 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
D45V3, multiclass
D45V4, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               7               136
  CLUS_2               2                83
  CLUS_3               1               148
D45V5, multiclass
D45V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1    2
  3Q LOSS WILD-TYPE  120   71
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1               120
  CLUS_2               2                71
D45V7, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               8               134
  CLUS_2               1               106
  CLUS_3               0               113
D45V8, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                65
  CLUS_2               0                92
  CLUS_3               0                65
  CLUS_4               9               131
D45V9, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               8               186
  CLUS_2               2               144
  CLUS_3               0               139
D45V10, multiclass

Clustering(46) Variable = 4p loss mutation analysis
D46V1, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               5                13
  CLUS_3               0                14
  CLUS_4               0                 8
D46V2, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               0                20
  CLUS_2               1                14
  CLUS_3               5                13
D46V3, multiclass
D46V4, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              41               102
  CLUS_2              15                70
  CLUS_3               3               146
D46V5, multiclass
D46V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      7    7
  4P LOSS WILD-TYPE  114   66
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               7               114
  CLUS_2               7                66
D46V7, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              30               112
  CLUS_2               1               106
  CLUS_3               3               110
D46V8, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               2                63
  CLUS_2               1                91
  CLUS_3               2                63
  CLUS_4              29               111
D46V9, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              53               141
  CLUS_2               4               142
  CLUS_3               6               133
D46V10, multiclass

Clustering(47) Variable = 4q loss mutation analysis
D47V1, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               2                16
  CLUS_3               0                14
  CLUS_4               0                 8
D47V2, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               0                20
  CLUS_2               1                14
  CLUS_3               2                16
D47V3, multiclass
D47V4, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              39               104
  CLUS_2              16                69
  CLUS_3               2               147
D47V5, multiclass
D47V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      8    6
  4Q LOSS WILD-TYPE  113   67
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               8               113
  CLUS_2               6                67
D47V7, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              27               115
  CLUS_2               0               107
  CLUS_3               5               108
D47V8, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               2                63
  CLUS_2               0                92
  CLUS_3               2                63
  CLUS_4              28               112
D47V9, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              49               145
  CLUS_2               6               140
  CLUS_3               6               133
D47V10, multiclass

Clustering(48) Variable = 5p loss mutation analysis
D48V1, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               3                15
  CLUS_3               0                14
  CLUS_4               0                 8
D48V2, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               0                20
  CLUS_2               1                14
  CLUS_3               3                15
D48V3, multiclass
D48V4, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              15               128
  CLUS_2               4                81
  CLUS_3               1               148
D48V5, multiclass
D48V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      4    6
  5P LOSS WILD-TYPE  117   67
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               4               117
  CLUS_2               6                67
D48V7, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              13               129
  CLUS_2               0               107
  CLUS_3               3               110
D48V8, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               0                65
  CLUS_2               0                92
  CLUS_3               3                62
  CLUS_4              13               127
D48V9, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              20               174
  CLUS_2               3               143
  CLUS_3               4               135
D48V10, multiclass

Clustering(49) Variable = 5q loss mutation analysis
D49V1, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               5                13
  CLUS_3               0                14
  CLUS_4               0                 8
D49V2, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                20
  CLUS_2               1                14
  CLUS_3               5                13
D49V3, multiclass
D49V4, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              29               114
  CLUS_2               6                79
  CLUS_3               1               148
D49V5, multiclass
D49V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      6    8
  5Q LOSS WILD-TYPE  115   65
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               6               115
  CLUS_2               8                65
D49V7, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              25               117
  CLUS_2               1               106
  CLUS_3               2               111
D49V8, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                65
  CLUS_2               0                92
  CLUS_3               3                62
  CLUS_4              25               115
D49V9, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              35               159
  CLUS_2               4               142
  CLUS_3               5               134
D49V10, multiclass

Clustering(50) Variable = 6p loss mutation analysis
D50V1, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               2                16
  CLUS_3               0                14
  CLUS_4               0                 8
D50V2, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               0                20
  CLUS_2               1                14
  CLUS_3               2                16
D50V3, multiclass
D50V4, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               4               139
  CLUS_2               2                83
  CLUS_3               0               149
D50V5, multiclass
D50V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1    2
  6P LOSS WILD-TYPE  120   71
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1               120
  CLUS_2               2                71
D50V7, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               4               138
  CLUS_2               0               107
  CLUS_3               1               112
D50V8, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1                64
  CLUS_2               0                92
  CLUS_3               0                65
  CLUS_4               4               136
D50V9, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               7               187
  CLUS_2               1               145
  CLUS_3               0               139
D50V10, multiclass

Clustering(51) Variable = 6q loss mutation analysis
D51V1, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               2                16
  CLUS_3               0                14
  CLUS_4               0                 8
D51V2, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               0                20
  CLUS_2               1                14
  CLUS_3               2                16
D51V3, multiclass
D51V4, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               5               138
  CLUS_2               3                82
  CLUS_3               0               149
D51V5, multiclass
D51V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1    2
  6Q LOSS WILD-TYPE  120   71
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               1               120
  CLUS_2               2                71
D51V7, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               7               135
  CLUS_2               0               107
  CLUS_3               1               112
D51V8, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               1                64
  CLUS_2               0                92
  CLUS_3               0                65
  CLUS_4               7               133
D51V9, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               8               186
  CLUS_2               1               145
  CLUS_3               1               138
D51V10, multiclass

Clustering(52) Variable = 7p loss mutation analysis
D52V1, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0                13
  CLUS_2               3                15
  CLUS_3               0                14
  CLUS_4               0                 8
D52V2, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0                20
  CLUS_2               0                15
  CLUS_3               3                15
D52V3, multiclass
D52V4, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              15               128
  CLUS_2               7                78
  CLUS_3               3               146
D52V5, multiclass
D52V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2    4
  7P LOSS WILD-TYPE  119   69
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               2               119
  CLUS_2               4                69
D52V7, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              18               124
  CLUS_2               2               105
  CLUS_3               2               111
D52V8, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               2                63
  CLUS_2               0                92
  CLUS_3               1                64
  CLUS_4              19               121
D52V9, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              20               174
  CLUS_2               5               141
  CLUS_3               4               135
D52V10, multiclass

Clustering(53) Variable = 7q loss mutation analysis
D53V1, multiclass
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
clus
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-B5-A0JR        TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-B5-A0K4        TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
D53V2, multiclass
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
clus
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-B5-A0JR        TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-B5-A0K4        TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
D53V3, multiclass
D53V4, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              16               127
  CLUS_2               6                79
  CLUS_3               1               148
D53V5, multiclass
D53V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1    6
  7Q LOSS WILD-TYPE  120   67
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               1               120
  CLUS_2               6                67
D53V7, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              17               125
  CLUS_2               0               107
  CLUS_3               0               113
D53V8, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               0                65
  CLUS_2               0                92
  CLUS_3               0                65
  CLUS_4              17               123
D53V9, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              20               174
  CLUS_2               3               143
  CLUS_3               4               135
D53V10, multiclass

Clustering(54) Variable = 8p loss mutation analysis
D54V1, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                13
  CLUS_2               5                13
  CLUS_3               0                14
  CLUS_4               0                 8
D54V2, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                20
  CLUS_2               0                15
  CLUS_3               5                13
D54V3, multiclass
D54V4, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              37               106
  CLUS_2               8                77
  CLUS_3               1               148
D54V5, multiclass
D54V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4    6
  8P LOSS WILD-TYPE  117   67
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               4               117
  CLUS_2               6                67
D54V7, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              30               112
  CLUS_2               0               107
  CLUS_3               1               112
D54V8, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               1                64
  CLUS_2               0                92
  CLUS_3               1                64
  CLUS_4              29               111
D54V9, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              45               149
  CLUS_2               1               145
  CLUS_3               4               135
D54V10, multiclass

Clustering(55) Variable = 8q loss mutation analysis
D55V1, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05H 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D55V2, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05H 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D55V3, multiclass
D55V4, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               9               134
  CLUS_2               1                84
  CLUS_3               0               149
D55V5, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0G9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0GG        TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0GM        TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0R6        TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0RA        TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A059        TCGA-AP-A05A        TCGA-AP-A05H        TCGA-AP-A05J 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P        TCGA-AP-A0LD 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG        TCGA-AP-A0LH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL        TCGA-AP-A0LM 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT        TCGA-AP-A0LV 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06D 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L        TCGA-AX-A0IS 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0        TCGA-AX-A0J1 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B5-A0JT        TCGA-B5-A0JY        TCGA-B5-A0JZ        TCGA-B5-A0K0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B5-A0K1        TCGA-B5-A0K2        TCGA-B5-A0K3        TCGA-B5-A0K4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B5-A0K7        TCGA-B5-A0K9        TCGA-B5-A11E        TCGA-B5-A11F 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B5-A11G        TCGA-B5-A11H        TCGA-B5-A11I        TCGA-B5-A11N 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B5-A11Q        TCGA-B5-A11S        TCGA-B5-A11U        TCGA-B5-A11V 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B5-A11W        TCGA-B5-A11Y        TCGA-B5-A11Z        TCGA-B5-A121 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0LX        TCGA-BG-A0M0        TCGA-BG-A0M2 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BG-A0M3        TCGA-BG-A0M4        TCGA-BG-A0M6        TCGA-BG-A0M7 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BG-A0M8        TCGA-BG-A0M9        TCGA-BG-A0MC        TCGA-BG-A0MG 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BG-A0MS        TCGA-BG-A0MT        TCGA-BG-A0MU        TCGA-BG-A0RY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BG-A0VT        TCGA-BG-A0VV        TCGA-BG-A0W1        TCGA-BG-A0YU 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BG-A0YV        TCGA-BG-A186        TCGA-BG-A187        TCGA-BG-A18A 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BG-A18B        TCGA-BG-A18C        TCGA-BK-A0C9        TCGA-BK-A0CA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139        TCGA-BK-A13C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC        TCGA-BS-A0TD 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ        TCGA-BS-A0U7 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BS-A0U8        TCGA-BS-A0U9        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D55V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    1
  8Q LOSS WILD-TYPE  120   72
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               1               120
  CLUS_2               1                72
D55V7, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               4               138
  CLUS_2               0               107
  CLUS_3               0               113
D55V8, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                65
  CLUS_2               0                92
  CLUS_3               0                65
  CLUS_4               4               136
D55V9, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              10               184
  CLUS_2               0               146
  CLUS_3               1               138
D55V10, multiclass

Clustering(56) Variable = 9p loss mutation analysis
D56V1, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               6                12
  CLUS_3               0                14
  CLUS_4               0                 8
D56V2, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               0                20
  CLUS_2               1                14
  CLUS_3               6                12
D56V3, multiclass
D56V4, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              36               107
  CLUS_2              19                66
  CLUS_3               8               141
D56V5, multiclass
D56V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     11   11
  9P LOSS WILD-TYPE  110   62
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              11               110
  CLUS_2              11                62
D56V7, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              41               101
  CLUS_2               3               104
  CLUS_3               3               110
D56V8, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               0                65
  CLUS_2               1                91
  CLUS_3               3                62
  CLUS_4              43                97
D56V9, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              53               141
  CLUS_2              15               131
  CLUS_3               6               133
D56V10, multiclass

Clustering(57) Variable = 9q loss mutation analysis
D57V1, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               0                13
  CLUS_2               7                11
  CLUS_3               0                14
  CLUS_4               0                 8
D57V2, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               0                20
  CLUS_2               0                15
  CLUS_3               7                11
D57V3, multiclass
D57V4, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              46                97
  CLUS_2              21                64
  CLUS_3              12               137
D57V5, multiclass
D57V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     13   11
  9Q LOSS WILD-TYPE  108   62
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              13               108
  CLUS_2              11                62
D57V7, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              48                94
  CLUS_2               4               103
  CLUS_3               5               108
D57V8, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               0                65
  CLUS_2               2                90
  CLUS_3               5                60
  CLUS_4              50                90
D57V9, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              66               128
  CLUS_2              17               129
  CLUS_3               8               131
D57V10, multiclass

Clustering(58) Variable = 10p loss mutation analysis
D58V1, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                3                 15
  CLUS_3                0                 14
  CLUS_4                0                  8
D58V2, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                0                 20
  CLUS_2                0                 15
  CLUS_3                3                 15
D58V3, multiclass
D58V4, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               15                128
  CLUS_2                4                 81
  CLUS_3                1                148
D58V5, multiclass
D58V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2    2
  10P LOSS WILD-TYPE  119   71
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                2                119
  CLUS_2                2                 71
D58V7, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               11                131
  CLUS_2                1                106
  CLUS_3                0                113
D58V8, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                0                 65
  CLUS_2                0                 92
  CLUS_3                1                 64
  CLUS_4               11                129
D58V9, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               20                174
  CLUS_2                1                145
  CLUS_3                1                138
D58V10, multiclass

Clustering(59) Variable = 10q loss mutation analysis
D59V1, multiclass
[1] "Remove cluster labels:" "10Q LOSS MUTATED"      
clus
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06F 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
D59V2, multiclass
[1] "Remove cluster labels:" "10Q LOSS MUTATED"      
clus
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06F 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
D59V3, multiclass
D59V4, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               16                127
  CLUS_2                5                 80
  CLUS_3                1                148
D59V5, multiclass
D59V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3    2
  10Q LOSS WILD-TYPE  118   71
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                3                118
  CLUS_2                2                 71
D59V7, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               11                131
  CLUS_2                1                106
  CLUS_3                0                113
D59V8, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                0                 65
  CLUS_2                0                 92
  CLUS_3                2                 63
  CLUS_4               10                130
D59V9, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               20                174
  CLUS_2                2                144
  CLUS_3                2                137
D59V10, multiclass

Clustering(60) Variable = 11p loss mutation analysis
D60V1, multiclass
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05D 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06F 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
D60V2, multiclass
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05D 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06F 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
D60V3, multiclass
D60V4, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               31                112
  CLUS_2               13                 72
  CLUS_3                4                145
D60V5, multiclass
D60V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      6    5
  11P LOSS WILD-TYPE  115   68
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                6                115
  CLUS_2                5                 68
D60V7, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               24                118
  CLUS_2                0                107
  CLUS_3                3                110
D60V8, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                 64
  CLUS_2                0                 92
  CLUS_3                2                 63
  CLUS_4               24                116
D60V9, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               42                152
  CLUS_2                6                140
  CLUS_3                3                136
D60V10, multiclass

Clustering(61) Variable = 11q loss mutation analysis
D61V1, multiclass
D61V2, multiclass
D61V3, multiclass
D61V4, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               26                117
  CLUS_2               12                 73
  CLUS_3                5                144
D61V5, multiclass
D61V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      5    2
  11Q LOSS WILD-TYPE  116   71
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                5                116
  CLUS_2                2                 71
D61V7, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               17                125
  CLUS_2                2                105
  CLUS_3                2                111
D61V8, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                1                 64
  CLUS_2                0                 92
  CLUS_3                1                 64
  CLUS_4               19                121
D61V9, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               35                159
  CLUS_2                6                140
  CLUS_3                3                136
D61V10, multiclass

Clustering(62) Variable = 12p loss mutation analysis
D62V1, multiclass
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06F 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
D62V2, multiclass
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06F 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
D62V3, multiclass
D62V4, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               16                127
  CLUS_2                5                 80
  CLUS_3                1                148
D62V5, multiclass
D62V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      4    3
  12P LOSS WILD-TYPE  117   70
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                4                117
  CLUS_2                3                 70
D62V7, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               12                130
  CLUS_2                0                107
  CLUS_3                0                113
D62V8, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                0                 65
  CLUS_2                0                 92
  CLUS_3                2                 63
  CLUS_4               10                130
D62V9, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               23                171
  CLUS_2                1                145
  CLUS_3                0                139
D62V10, multiclass

Clustering(63) Variable = 12q loss mutation analysis
D63V1, multiclass
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0IW 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BK-A0CC 
"12Q LOSS WILD-TYPE" 
D63V2, multiclass
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0IW 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BK-A0CC 
"12Q LOSS WILD-TYPE" 
D63V3, multiclass
D63V4, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               13                130
  CLUS_2                3                 82
  CLUS_3                0                149
D63V5, multiclass
D63V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3    4
  12Q LOSS WILD-TYPE  118   69
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                3                118
  CLUS_2                4                 69
D63V7, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                8                134
  CLUS_2                0                107
  CLUS_3                0                113
D63V8, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                0                 65
  CLUS_2                0                 92
  CLUS_3                0                 65
  CLUS_4                8                132
D63V9, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               17                177
  CLUS_2                0                146
  CLUS_3                0                139
D63V10, multiclass

Clustering(64) Variable = 13q loss mutation analysis
D64V1, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                2                 16
  CLUS_3                0                 14
  CLUS_4                0                  8
D64V2, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                0                 20
  CLUS_2                1                 14
  CLUS_3                2                 16
D64V3, multiclass
D64V4, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               31                112
  CLUS_2               14                 71
  CLUS_3                8                141
D64V5, multiclass
D64V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      7    7
  13Q LOSS WILD-TYPE  114   66
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                7                114
  CLUS_2                7                 66
D64V7, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               23                119
  CLUS_2                3                104
  CLUS_3                6                107
D64V8, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                3                 62
  CLUS_2                1                 91
  CLUS_3                2                 63
  CLUS_4               26                114
D64V9, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               39                155
  CLUS_2               10                136
  CLUS_3                9                130
D64V10, multiclass

Clustering(65) Variable = 14q loss mutation analysis
D65V1, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                5                 13
  CLUS_3                0                 14
  CLUS_4                0                  8
D65V2, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                0                 20
  CLUS_2                0                 15
  CLUS_3                5                 13
D65V3, multiclass
D65V4, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               27                116
  CLUS_2                5                 80
  CLUS_3                0                149
D65V5, multiclass
D65V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      3   10
  14Q LOSS WILD-TYPE  118   63
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                3                118
  CLUS_2               10                 63
D65V7, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               23                119
  CLUS_2                0                107
  CLUS_3                2                111
D65V8, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                1                 64
  CLUS_2                0                 92
  CLUS_3                1                 64
  CLUS_4               23                117
D65V9, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               30                164
  CLUS_2                1                145
  CLUS_3                8                131
D65V10, multiclass

Clustering(66) Variable = 15q loss mutation analysis
D66V1, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                6                 12
  CLUS_3                0                 14
  CLUS_4                0                  8
D66V2, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                 20
  CLUS_2                0                 15
  CLUS_3                6                 12
D66V3, multiclass
D66V4, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               51                 92
  CLUS_2               16                 69
  CLUS_3                4                145
D66V5, multiclass
D66V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      7    8
  15Q LOSS WILD-TYPE  114   65
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                7                114
  CLUS_2                8                 65
D66V7, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               36                106
  CLUS_2                2                105
  CLUS_3                5                108
D66V8, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                 64
  CLUS_2                1                 91
  CLUS_3                4                 61
  CLUS_4               37                103
D66V9, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               64                130
  CLUS_2                7                139
  CLUS_3                7                132
D66V10, multiclass

Clustering(67) Variable = 16p loss mutation analysis
D67V1, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                5                 13
  CLUS_3                0                 14
  CLUS_4                0                  8
D67V2, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                 20
  CLUS_2                0                 15
  CLUS_3                5                 13
D67V3, multiclass
D67V4, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               38                105
  CLUS_2               17                 68
  CLUS_3                4                145
D67V5, multiclass
D67V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     10    7
  16P LOSS WILD-TYPE  111   66
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               10                111
  CLUS_2                7                 66
D67V7, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               35                107
  CLUS_2                2                105
  CLUS_3                4                109
D67V8, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                3                 62
  CLUS_2                1                 91
  CLUS_3                2                 63
  CLUS_4               35                105
D67V9, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               49                145
  CLUS_2                6                140
  CLUS_3               10                129
D67V10, multiclass

Clustering(68) Variable = 16q loss mutation analysis
D68V1, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                7                 11
  CLUS_3                1                 13
  CLUS_4                0                  8
D68V2, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                0                 15
  CLUS_3                7                 11
D68V3, multiclass
D68V4, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               58                 85
  CLUS_2               25                 60
  CLUS_3               11                138
D68V5, multiclass
D68V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     18   10
  16Q LOSS WILD-TYPE  103   63
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               18                103
  CLUS_2               10                 63
D68V7, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               54                 88
  CLUS_2                6                101
  CLUS_3               11                102
D68V8, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                9                 56
  CLUS_2                4                 88
  CLUS_3                6                 59
  CLUS_4               52                 88
D68V9, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               75                119
  CLUS_2               11                135
  CLUS_3               19                120
D68V10, multiclass

Clustering(69) Variable = 17p loss mutation analysis
D69V1, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                7                 11
  CLUS_3                1                 13
  CLUS_4                0                  8
D69V2, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                0                 15
  CLUS_3                7                 11
D69V3, multiclass
D69V4, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               61                 82
  CLUS_2               18                 67
  CLUS_3               10                139
D69V5, multiclass
D69V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     15   11
  17P LOSS WILD-TYPE  106   62
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               15                106
  CLUS_2               11                 62
D69V7, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               58                 84
  CLUS_2                2                105
  CLUS_3                4                109
D69V8, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                1                 64
  CLUS_2                0                 92
  CLUS_3                5                 60
  CLUS_4               58                 82
D69V9, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               78                116
  CLUS_2               14                132
  CLUS_3                9                130
D69V10, multiclass

Clustering(70) Variable = 17q loss mutation analysis
D70V1, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                5                 13
  CLUS_3                0                 14
  CLUS_4                0                  8
D70V2, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                 20
  CLUS_2                0                 15
  CLUS_3                5                 13
D70V3, multiclass
D70V4, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               35                108
  CLUS_2               14                 71
  CLUS_3                9                140
D70V5, multiclass
D70V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     10    8
  17Q LOSS WILD-TYPE  111   65
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               10                111
  CLUS_2                8                 65
D70V7, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               33                109
  CLUS_2                2                105
  CLUS_3                4                109
D70V8, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                 64
  CLUS_2                0                 92
  CLUS_3                3                 62
  CLUS_4               35                105
D70V9, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               46                148
  CLUS_2               11                135
  CLUS_3                7                132
D70V10, multiclass

Clustering(71) Variable = 18p loss mutation analysis
D71V1, multiclass
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LJ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
D71V2, multiclass
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LJ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
D71V3, multiclass
D71V4, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               22                121
  CLUS_2                6                 79
  CLUS_3                2                147
D71V5, multiclass
D71V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      7    3
  18P LOSS WILD-TYPE  114   70
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                7                114
  CLUS_2                3                 70
D71V7, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               17                125
  CLUS_2                1                106
  CLUS_3                4                109
D71V8, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                1                 64
  CLUS_2                0                 92
  CLUS_3                4                 61
  CLUS_4               17                123
D71V9, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               23                171
  CLUS_2                4                142
  CLUS_3                7                132
D71V10, multiclass

Clustering(72) Variable = 18q loss mutation analysis
D72V1, multiclass
[1] "Remove cluster labels:" "18Q LOSS MUTATED"      
clus
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LJ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
D72V2, multiclass
[1] "Remove cluster labels:" "18Q LOSS MUTATED"      
clus
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LJ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
D72V3, multiclass
D72V4, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               30                113
  CLUS_2               10                 75
  CLUS_3                4                145
D72V5, multiclass
D72V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      8    4
  18Q LOSS WILD-TYPE  113   69
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                8                113
  CLUS_2                4                 69
D72V7, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               23                119
  CLUS_2                1                106
  CLUS_3                4                109
D72V8, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                 64
  CLUS_2                0                 92
  CLUS_3                3                 62
  CLUS_4               24                116
D72V9, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               36                158
  CLUS_2                5                141
  CLUS_3                6                133
D72V10, multiclass

Clustering(73) Variable = 19p loss mutation analysis
D73V1, multiclass
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0IW 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BK-A0CC 
"19P LOSS WILD-TYPE" 
D73V2, multiclass
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0IW 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BK-A0CC 
"19P LOSS WILD-TYPE" 
D73V3, multiclass
D73V4, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               25                118
  CLUS_2                4                 81
  CLUS_3                1                148
D73V5, multiclass
D73V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      5    3
  19P LOSS WILD-TYPE  116   70
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                5                116
  CLUS_2                3                 70
D73V7, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               16                126
  CLUS_2                0                107
  CLUS_3                2                111
D73V8, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                1                 64
  CLUS_2                0                 92
  CLUS_3                0                 65
  CLUS_4               17                123
D73V9, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               26                168
  CLUS_2                2                144
  CLUS_3                4                135
D73V10, multiclass

Clustering(74) Variable = 19q loss mutation analysis
D74V1, multiclass
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LJ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
D74V2, multiclass
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LJ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
D74V3, multiclass
D74V4, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               18                125
  CLUS_2                5                 80
  CLUS_3                1                148
D74V5, multiclass
D74V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      5    2
  19Q LOSS WILD-TYPE  116   71
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                5                116
  CLUS_2                2                 71
D74V7, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               12                130
  CLUS_2                0                107
  CLUS_3                2                111
D74V8, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                 64
  CLUS_2                0                 92
  CLUS_3                1                 64
  CLUS_4               12                128
D74V9, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               19                175
  CLUS_2                2                144
  CLUS_3                5                134
D74V10, multiclass

Clustering(75) Variable = 20p loss mutation analysis
D75V1, multiclass
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G5         TCGA-A5-A0GA         TCGA-A5-A0GB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05P 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A0L8         TCGA-AP-A0L9         TCGA-AP-A0LD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LJ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
D75V2, multiclass
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G5         TCGA-A5-A0GA         TCGA-A5-A0GB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05P 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A0L8         TCGA-AP-A0L9         TCGA-AP-A0LD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LJ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
D75V3, multiclass
D75V4, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                6                137
  CLUS_2                3                 82
  CLUS_3                1                148
D75V5, multiclass
D75V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2    2
  20P LOSS WILD-TYPE  119   71
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                119
  CLUS_2                2                 71
D75V7, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                7                135
  CLUS_2                0                107
  CLUS_3                2                111
D75V8, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                 63
  CLUS_2                0                 92
  CLUS_3                0                 65
  CLUS_4                7                133
D75V9, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1               11                183
  CLUS_2                0                146
  CLUS_3                2                137
D75V10, multiclass

Clustering(76) Variable = 20q loss mutation analysis
D76V1, multiclass
D76V2, multiclass
D76V3, multiclass
D76V4, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                3                140
  CLUS_2                3                 82
  CLUS_3                0                149
D76V5, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                192 
        TCGA-A5-A0G1         TCGA-A5-A0G2         TCGA-A5-A0G5 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A5-A0G9         TCGA-A5-A0GA         TCGA-A5-A0GB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A5-A0GD         TCGA-A5-A0GE         TCGA-A5-A0GG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A5-A0GH         TCGA-A5-A0GI         TCGA-A5-A0GJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GQ         TCGA-A5-A0GR 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A5-A0GU         TCGA-A5-A0GV         TCGA-A5-A0GW 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A5-A0GX         TCGA-A5-A0R6         TCGA-A5-A0R7 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A5-A0R8         TCGA-A5-A0R9         TCGA-A5-A0RA 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A5-A0VP         TCGA-A5-A0VQ         TCGA-AP-A051 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A059         TCGA-AP-A05A 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05O         TCGA-AP-A05P 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LE         TCGA-AP-A0LF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LL         TCGA-AP-A0LM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LP         TCGA-AP-A0LT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A06D         TCGA-AX-A06F         TCGA-AX-A06J 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A06L         TCGA-AX-A0IS         TCGA-AX-A0IW 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A0IZ         TCGA-AX-A0J0         TCGA-AX-A0J1 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B5-A0JN         TCGA-B5-A0JT         TCGA-B5-A0JY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B5-A0JZ         TCGA-B5-A0K0         TCGA-B5-A0K1 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B5-A0K2         TCGA-B5-A0K3         TCGA-B5-A0K4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B5-A0K7         TCGA-B5-A0K9         TCGA-B5-A11E 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B5-A11F         TCGA-B5-A11G         TCGA-B5-A11H 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B5-A11I         TCGA-B5-A11N         TCGA-B5-A11Q 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B5-A11S         TCGA-B5-A11U         TCGA-B5-A11V 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B5-A11W         TCGA-B5-A11Y         TCGA-B5-A11Z 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B5-A121         TCGA-BG-A0LW         TCGA-BG-A0LX 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BG-A0M0         TCGA-BG-A0M2         TCGA-BG-A0M3 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BG-A0M4         TCGA-BG-A0M6         TCGA-BG-A0M7 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BG-A0M8         TCGA-BG-A0M9         TCGA-BG-A0MC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BG-A0MG         TCGA-BG-A0MS         TCGA-BG-A0MT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BG-A0MU         TCGA-BG-A0RY         TCGA-BG-A0VT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BG-A0VV         TCGA-BG-A0W1         TCGA-BG-A0YU 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BG-A0YV         TCGA-BG-A186         TCGA-BG-A187 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BG-A18A         TCGA-BG-A18B         TCGA-BG-A18C 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BK-A0C9         TCGA-BK-A0CA         TCGA-BK-A0CB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BK-A0CC         TCGA-BK-A139         TCGA-BK-A13C 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BS-A0T9         TCGA-BS-A0TA         TCGA-BS-A0TC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BS-A0TD         TCGA-BS-A0TG         TCGA-BS-A0TI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BS-A0TJ         TCGA-BS-A0U7         TCGA-BS-A0U8 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BS-A0U9         TCGA-BS-A0UF         TCGA-BS-A0UJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BS-A0V7         TCGA-D1-A0ZP         TCGA-D1-A0ZR 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A0ZU         TCGA-D1-A101         TCGA-D1-A102 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A103         TCGA-D1-A15V         TCGA-D1-A15W 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A15X         TCGA-D1-A15Z         TCGA-D1-A160 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A161         TCGA-D1-A163         TCGA-D1-A165 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A167         TCGA-D1-A168         TCGA-D1-A169 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A16B         TCGA-D1-A16D         TCGA-D1-A16E 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A16G         TCGA-D1-A16I         TCGA-D1-A16J 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A16N         TCGA-D1-A16O         TCGA-D1-A16Q 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A16R         TCGA-D1-A16S         TCGA-D1-A16V 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A16X         TCGA-D1-A16Y         TCGA-D1-A175 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A176         TCGA-D1-A177         TCGA-D1-A179 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A17B         TCGA-D1-A17C         TCGA-D1-A17D 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A17F         TCGA-D1-A17H         TCGA-D1-A17K 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A17L         TCGA-D1-A17M         TCGA-D1-A17N 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A17Q         TCGA-D1-A17R         TCGA-D1-A17S 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A17T         TCGA-D1-A17U         TCGA-DI-A0WH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D76V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    0
  20Q LOSS WILD-TYPE  119   73
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                2                119
  CLUS_2                0                 73
D76V7, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                3                139
  CLUS_2                0                107
  CLUS_3                1                112
D76V8, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                1                 64
  CLUS_2                0                 92
  CLUS_3                0                 65
  CLUS_4                3                137
D76V9, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                5                189
  CLUS_2                0                146
  CLUS_3                1                138
D76V10, multiclass

Clustering(77) Variable = 21q loss mutation analysis
D77V1, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                4                 14
  CLUS_3                0                 14
  CLUS_4                0                  8
D77V2, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                0                 20
  CLUS_2                0                 15
  CLUS_3                4                 14
D77V3, multiclass
D77V4, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               17                126
  CLUS_2                5                 80
  CLUS_3                3                146
D77V5, multiclass
D77V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      6    5
  21Q LOSS WILD-TYPE  115   68
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                6                115
  CLUS_2                5                 68
D77V7, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               15                127
  CLUS_2                0                107
  CLUS_3                3                110
D77V8, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                1                 64
  CLUS_2                0                 92
  CLUS_3                3                 62
  CLUS_4               14                126
D77V9, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               20                174
  CLUS_2                2                144
  CLUS_3                7                132
D77V10, multiclass

Clustering(78) Variable = 22q loss mutation analysis
D78V1, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                5                 13
  CLUS_3                0                 14
  CLUS_4                0                  8
D78V2, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                0                 20
  CLUS_2                0                 15
  CLUS_3                5                 13
D78V3, multiclass
D78V4, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               46                 97
  CLUS_2               22                 63
  CLUS_3               10                139
D78V5, multiclass
D78V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     13    7
  22Q LOSS WILD-TYPE  108   66
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               13                108
  CLUS_2                7                 66
D78V7, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               41                101
  CLUS_2                3                104
  CLUS_3                5                108
D78V8, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                1                 64
  CLUS_2                1                 91
  CLUS_3                3                 62
  CLUS_4               44                 96
D78V9, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               61                133
  CLUS_2               14                132
  CLUS_3                9                130
D78V10, multiclass

Clustering(79) Variable = Xq loss mutation analysis
D79V1, multiclass
D79V2, multiclass
D79V3, multiclass
D79V4, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              11               132
  CLUS_2               5                80
  CLUS_3               0               149
D79V5, multiclass
D79V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2    2
  XQ LOSS WILD-TYPE  119   71
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               2               119
  CLUS_2               2                71
D79V7, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               7               135
  CLUS_2               0               107
  CLUS_3               1               112
D79V8, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                65
  CLUS_2               0                92
  CLUS_3               0                65
  CLUS_4               8               132
D79V9, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              15               179
  CLUS_2               1               145
  CLUS_3               2               137
D79V10, multiclass
                     V1                      V2                      V3 
            "MRNA_CNMF"    "MRNA_CHIERARCHICAL"               "CN_CNMF" 
                     V4                      V5                      V6 
     "METHLYATION_CNMF"             "RPPA_CNMF"    "RPPA_CHIERARCHICAL" 
                     V7                      V8                      V9 
         "MRNASEQ_CNMF" "MRNASEQ_CHIERARCHICAL"           "MIRSEQ_CNMF" 
                    V10 
 "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
