
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/376092/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/LUAD-TP/2909298/1.GDAC_mergedClustering.Finished/LUAD-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=LUAD-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=LUAD-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=477, in cluster file=472, common to both=472
[1]  80 472
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               58               414 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               58               414 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              177               295 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              177               295 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               50               422 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               50               422 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               45               427 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               45               427 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               13               459 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               13               459 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               29               443 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               29               443 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               30               442 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               30               442 
[1] "4q gain mutation analysis"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               11               461 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               11               461 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              178               294 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              178               294 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               56               416 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               56               416 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               71               401 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               71               401 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               20               452 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               20               452 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              154               318 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              154               318 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              111               361 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              111               361 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               59               413 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               59               413 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              144               328 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              144               328 
[1] "9p gain mutation analysis"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               14               458 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               14               458 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                7               465 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                7               465 
[1] "10p gain mutation analysis"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                49                423 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                49                423 
[1] "10q gain mutation analysis"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                28                444 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                28                444 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                35                437 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                35                437 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                51                421 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                51                421 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                57                415 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                57                415 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                46                426 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                46                426 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                15                457 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                15                457 
[1] "14q gain mutation analysis"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                56                416 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                56                416 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                14                458 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                14                458 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                67                405 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                67                405 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                42                430 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                42                430 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                28                444 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                28                444 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                78                394 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                78                394 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                42                430 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                42                430 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                26                446 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                26                446 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 6                466 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 6                466 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                22                450 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                22                450 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                61                411 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                61                411 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                76                396 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                76                396 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                41                431 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                41                431 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                20                452 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                20                452 
[1] "Xq gain mutation analysis"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               19               453 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               19               453 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               28               444 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               28               444 
[1] "1q loss mutation analysis"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               11               461 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               11               461 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                6               466 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                6               466 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                4               468 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                4               468 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               93               379 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               93               379 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               56               416 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               56               416 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               38               434 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               38               434 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               45               427 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               45               427 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               15               457 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               15               457 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               58               414 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               58               414 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               38               434 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               38               434 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              105               367 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              105               367 
[1] "7p loss mutation analysis"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               14               458 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               14               458 
[1] "7q loss mutation analysis"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               17               455 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               17               455 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              118               354 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              118               354 
[1] "8q loss mutation analysis"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               17               455 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               17               455 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              139               333 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              139               333 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              117               355 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              117               355 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                35                437 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                35                437 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                45                427 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                45                427 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                32                440 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                32                440 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                29                443 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                29                443 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                37                435 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                37                435 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                23                449 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                23                449 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               109                363 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               109                363 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                46                426 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                46                426 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                95                377 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                95                377 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                37                435 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                37                435 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                56                416 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                56                416 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               109                363 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               109                363 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                17                455 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                17                455 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                75                397 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                75                397 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               108                364 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               108                364 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               112                360 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               112                360 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                67                405 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                67                405 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                61                411 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                61                411 
[1] "20q loss mutation analysis"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                24                448 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                24                448 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                66                406 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                66                406 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                90                382 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                90                382 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               11               461 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               11               461 
[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 472 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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[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 472 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=4, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=5, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=5, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain mutation analysis
D1V1, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               1                 8
  CLUS_3               2                10
  CLUS_4               1                 5
D1V2, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               2                11
  CLUS_3               1                11
D1V3, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              39               109
  CLUS_2               9               179
  CLUS_3               6                81
  CLUS_4               4                45
D1V4, multiclass
D1V5, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              14                71
  CLUS_2               4                71
  CLUS_3               8                67
D1V6, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1                22
  CLUS_2              17                72
  CLUS_3               3                62
  CLUS_4               5                53
D1V7, multiclass
D1V8, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              19               133
  CLUS_2              10                95
  CLUS_3              15                80
D1V9, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              16               142
  CLUS_2              25               158
  CLUS_3               8                49
D1V10, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              20               143
  CLUS_2              13               102
  CLUS_3              16               104

Clustering(2) Variable = 1q gain mutation analysis
D2V1, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               3                 6
  CLUS_3               5                 7
  CLUS_4               2                 4
D2V2, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                 5
  CLUS_2               5                 8
  CLUS_3               3                 9
D2V3, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              67                81
  CLUS_2              59               129
  CLUS_3              29                58
  CLUS_4              22                27
D2V4, multiclass
D2V5, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              30                55
  CLUS_2              33                42
  CLUS_3              21                54
D2V6, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               5                18
  CLUS_2              34                55
  CLUS_3              19                46
  CLUS_4              26                32
D2V7, multiclass
D2V8, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              65                87
  CLUS_2              38                67
  CLUS_3              33                62
D2V9, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              64                94
  CLUS_2              69               114
  CLUS_3              18                39
D2V10, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              69                94
  CLUS_2              35                80
  CLUS_3              47                73

Clustering(3) Variable = 2p gain mutation analysis
D3V1, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               2                 3
  CLUS_2               0                 9
  CLUS_3               1                11
  CLUS_4               3                 3
D3V2, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               4                 3
  CLUS_2               1                12
  CLUS_3               1                11
D3V3, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              21               127
  CLUS_2               3               185
  CLUS_3              15                72
  CLUS_4              11                38
D3V4, multiclass
D3V5, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               7                78
  CLUS_2               8                67
  CLUS_3              15                60
D3V6, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               1                22
  CLUS_2               7                82
  CLUS_3              15                50
  CLUS_4               7                51
D3V7, multiclass
D3V8, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              12               140
  CLUS_2              24                81
  CLUS_3               7                88
D3V9, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              10               148
  CLUS_2              32               151
  CLUS_3               3                54
D3V10, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              11               152
  CLUS_2              11               104
  CLUS_3              23                97

Clustering(4) Variable = 2q gain mutation analysis
D4V1, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               0                 9
  CLUS_3               1                11
  CLUS_4               3                 3
D4V2, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               3                 4
  CLUS_2               1                12
  CLUS_3               0                12
D4V3, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              13               135
  CLUS_2               5               183
  CLUS_3              15                72
  CLUS_4              12                37
D4V4, multiclass
D4V5, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               5                80
  CLUS_2               9                66
  CLUS_3              10                65
D4V6, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               1                22
  CLUS_2               6                83
  CLUS_3              10                55
  CLUS_4               7                51
D4V7, multiclass
D4V8, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              14               138
  CLUS_2              17                88
  CLUS_3               4                91
D4V9, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              10               148
  CLUS_2              28               155
  CLUS_3               2                55
D4V10, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              11               152
  CLUS_2              10               105
  CLUS_3              19               101

Clustering(5) Variable = 3p gain mutation analysis
D5V1, multiclass
D5V2, multiclass
D5V3, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               6               142
  CLUS_2               1               187
  CLUS_3               5                82
  CLUS_4               1                48
D5V4, multiclass
D5V5, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               4                81
  CLUS_2               0                75
  CLUS_3               4                71
D5V6, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               0                23
  CLUS_2               2                87
  CLUS_3               5                60
  CLUS_4               1                57
D5V7, multiclass
D5V8, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2               150
  CLUS_2               4               101
  CLUS_3               5                90
D5V9, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               4               154
  CLUS_2               7               176
  CLUS_3               1                56
D5V10, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3               160
  CLUS_2               6               109
  CLUS_3               3               117

Clustering(6) Variable = 3q gain mutation analysis
D6V1, multiclass
[1] "Remove cluster labels:" "3Q GAIN MUTATED"       
clus
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-55-1595        TCGA-55-1596        TCGA-64-1676        TCGA-64-1677 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
D6V2, multiclass
[1] "Remove cluster labels:" "3Q GAIN MUTATED"       
clus
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-55-1595        TCGA-55-1596        TCGA-64-1676        TCGA-64-1677 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
D6V3, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              10               138
  CLUS_2               4               184
  CLUS_3              12                75
  CLUS_4               3                46
D6V4, multiclass
D6V5, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               5                80
  CLUS_2               2                73
  CLUS_3               9                66
D6V6, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               0                23
  CLUS_2               3                86
  CLUS_3              10                55
  CLUS_4               3                55
D6V7, multiclass
D6V8, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               7               145
  CLUS_2               8                97
  CLUS_3               7                88
D6V9, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               7               151
  CLUS_2              16               167
  CLUS_3               1                56
D6V10, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               6               157
  CLUS_2               8               107
  CLUS_3              10               110

Clustering(7) Variable = 4p gain mutation analysis
D7V1, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               0                 9
  CLUS_3               2                10
  CLUS_4               1                 5
D7V2, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               2                11
  CLUS_3               0                12
D7V3, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1              14               134
  CLUS_2               4               184
  CLUS_3              10                77
  CLUS_4               2                47
D7V4, multiclass
D7V5, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               7                78
  CLUS_2               2                73
  CLUS_3               9                66
D7V6, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0                23
  CLUS_2               8                81
  CLUS_3               9                56
  CLUS_4               1                57
D7V7, multiclass
D7V8, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               7               145
  CLUS_2               9                96
  CLUS_3              10                85
D7V9, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               8               150
  CLUS_2              17               166
  CLUS_3               2                55
D7V10, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               7               156
  CLUS_2              12               103
  CLUS_3               8               112

Clustering(8) Variable = 4q gain mutation analysis
D8V1, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1595        TCGA-55-1596        TCGA-64-1676 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-64-1677        TCGA-64-1678        TCGA-67-3770        TCGA-67-3771 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V2, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1595        TCGA-55-1596        TCGA-64-1676 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-64-1677        TCGA-64-1678        TCGA-67-3770        TCGA-67-3771 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V3, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               7               141
  CLUS_2               1               187
  CLUS_3               3                84
  CLUS_4               0                49
D8V4, multiclass
D8V5, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2                83
  CLUS_2               1                74
  CLUS_3               5                70
D8V6, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0                23
  CLUS_2               2                87
  CLUS_3               5                60
  CLUS_4               1                57
D8V7, multiclass
D8V8, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2               150
  CLUS_2               2               103
  CLUS_3               6                89
D8V9, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               1               157
  CLUS_2               7               176
  CLUS_3               2                55
D8V10, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               1               162
  CLUS_2               6               109
  CLUS_3               3               117

Clustering(9) Variable = 5p gain mutation analysis
D9V1, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               3                 2
  CLUS_2               2                 7
  CLUS_3               6                 6
  CLUS_4               2                 4
D9V2, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               3                 4
  CLUS_2               7                 6
  CLUS_3               3                 9
D9V3, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              93                55
  CLUS_2              39               149
  CLUS_3              24                63
  CLUS_4              22                27
D9V4, multiclass
D9V5, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              37                48
  CLUS_2              30                45
  CLUS_3              23                52
D9V6, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               6                17
  CLUS_2              35                54
  CLUS_3              27                38
  CLUS_4              22                36
D9V7, multiclass
D9V8, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              50               102
  CLUS_2              36                69
  CLUS_3              43                52
D9V9, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              54               104
  CLUS_2              73               110
  CLUS_3              23                34
D9V10, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              58               105
  CLUS_2              43                72
  CLUS_3              49                71

Clustering(10) Variable = 5q gain mutation analysis
D10V1, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               3                 2
  CLUS_2               0                 9
  CLUS_3               4                 8
  CLUS_4               0                 6
D10V2, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               4                 9
  CLUS_3               2                10
D10V3, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              25               123
  CLUS_2              17               171
  CLUS_3               6                81
  CLUS_4               8                41
D10V4, multiclass
D10V5, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              11                74
  CLUS_2              10                65
  CLUS_3               6                69
D10V6, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               0                23
  CLUS_2              12                77
  CLUS_3               6                59
  CLUS_4               9                49
D10V7, multiclass
D10V8, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              24               128
  CLUS_2               8                97
  CLUS_3               9                86
D10V9, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              18               140
  CLUS_2              17               166
  CLUS_3              11                46
D10V10, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              22               141
  CLUS_2              11               104
  CLUS_3              13               107

Clustering(11) Variable = 6p gain mutation analysis
D11V1, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1                 4
  CLUS_2               0                 9
  CLUS_3               3                 9
  CLUS_4               2                 4
D11V2, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               3                 4
  CLUS_2               3                10
  CLUS_3               0                12
D11V3, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              29               119
  CLUS_2              19               169
  CLUS_3              11                76
  CLUS_4              12                37
D11V4, multiclass
D11V5, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               6                79
  CLUS_2              18                57
  CLUS_3              10                65
D11V6, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2                21
  CLUS_2               9                80
  CLUS_3              11                54
  CLUS_4              12                46
D11V7, multiclass
D11V8, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              28               124
  CLUS_2              14                91
  CLUS_3              10                85
D11V9, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              23               135
  CLUS_2              32               151
  CLUS_3               4                53
D11V10, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              20               143
  CLUS_2              14               101
  CLUS_3              25                95

Clustering(12) Variable = 6q gain mutation analysis
D12V1, multiclass
D12V2, multiclass
D12V3, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               7               141
  CLUS_2               5               183
  CLUS_3               6                81
  CLUS_4               2                47
D12V4, multiclass
D12V5, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               1                84
  CLUS_2               3                72
  CLUS_3               6                69
D12V6, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               1                22
  CLUS_2               3                86
  CLUS_3               6                59
  CLUS_4               0                58
D12V7, multiclass
D12V8, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               4               148
  CLUS_2               5               100
  CLUS_3               4                91
D12V9, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               3               155
  CLUS_2              13               170
  CLUS_3               2                55
D12V10, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               2               161
  CLUS_2               4               111
  CLUS_3              12               108

Clustering(13) Variable = 7p gain mutation analysis
D13V1, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               1                 4
  CLUS_2               2                 7
  CLUS_3               3                 9
  CLUS_4               0                 6
D13V2, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               3                10
  CLUS_3               3                 9
D13V3, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              89                59
  CLUS_2              26               162
  CLUS_3              28                59
  CLUS_4              11                38
D13V4, multiclass
D13V5, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              38                47
  CLUS_2              13                62
  CLUS_3              35                40
D13V6, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               5                18
  CLUS_2              41                48
  CLUS_3              27                38
  CLUS_4              13                45
D13V7, multiclass
D13V8, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              38               114
  CLUS_2              33                72
  CLUS_3              49                46
D13V9, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              40               118
  CLUS_2              66               117
  CLUS_3              30                27
D13V10, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              42               121
  CLUS_2              52                63
  CLUS_3              42                78

Clustering(14) Variable = 7q gain mutation analysis
D14V1, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               3                 6
  CLUS_3               1                11
  CLUS_4               1                 5
D14V2, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               1                12
  CLUS_3               3                 9
D14V3, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              61                87
  CLUS_2              22               166
  CLUS_3              20                67
  CLUS_4               8                41
D14V4, multiclass
D14V5, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              28                57
  CLUS_2              13                62
  CLUS_3              19                56
D14V6, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               4                19
  CLUS_2              29                60
  CLUS_3              14                51
  CLUS_4              13                45
D14V7, multiclass
D14V8, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              27               125
  CLUS_2              22                83
  CLUS_3              40                55
D14V9, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              32               126
  CLUS_2              46               137
  CLUS_3              21                36
D14V10, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              33               130
  CLUS_2              37                78
  CLUS_3              29                91

Clustering(15) Variable = 8p gain mutation analysis
D15V1, multiclass
[1] "Remove cluster labels:" "8P GAIN MUTATED"       
clus
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                2                30 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1595        TCGA-64-1676        TCGA-64-1677 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-64-1678        TCGA-67-3770        TCGA-67-3771        TCGA-67-3772 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-67-3773        TCGA-67-3774 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
D15V2, multiclass
[1] "Remove cluster labels:" "8P GAIN MUTATED"       
clus
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                2                30 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1595        TCGA-64-1676        TCGA-64-1677 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-64-1678        TCGA-67-3770        TCGA-67-3771        TCGA-67-3772 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-67-3773        TCGA-67-3774 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
D15V3, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              14               134
  CLUS_2              11               177
  CLUS_3              11                76
  CLUS_4              23                26
D15V4, multiclass
D15V5, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              13                72
  CLUS_2               8                67
  CLUS_3              12                63
D15V6, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               2                21
  CLUS_2              12                77
  CLUS_3              11                54
  CLUS_4               8                50
D15V7, multiclass
D15V8, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              16               136
  CLUS_2              20                85
  CLUS_3               5                90
D15V9, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              16               142
  CLUS_2              20               163
  CLUS_3               7                50
D15V10, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              18               145
  CLUS_2               7               108
  CLUS_3              18               102

Clustering(16) Variable = 8q gain mutation analysis
D16V1, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1                 4
  CLUS_2               3                 6
  CLUS_3               1                11
  CLUS_4               4                 2
D16V2, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               4                 3
  CLUS_2               2                11
  CLUS_3               3                 9
D16V3, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              56                92
  CLUS_2              17               171
  CLUS_3              34                53
  CLUS_4              37                12
D16V4, multiclass
D16V5, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              30                55
  CLUS_2              16                59
  CLUS_3              30                45
D16V6, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               4                19
  CLUS_2              36                53
  CLUS_3              26                39
  CLUS_4              10                48
D16V7, multiclass
D16V8, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              32               120
  CLUS_2              44                61
  CLUS_3              31                64
D16V9, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              27               131
  CLUS_2              73               110
  CLUS_3              18                39
D16V10, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              31               132
  CLUS_2              33                82
  CLUS_3              54                66

Clustering(17) Variable = 9p gain mutation analysis
D17V1, multiclass
D17V2, multiclass
D17V3, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               9               139
  CLUS_2               1               187
  CLUS_3               3                84
  CLUS_4               1                48
D17V4, multiclass
D17V5, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2                83
  CLUS_2               2                73
  CLUS_3               1                74
D17V6, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               0                23
  CLUS_2               2                87
  CLUS_3               1                64
  CLUS_4               2                56
D17V7, multiclass
D17V8, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               4               148
  CLUS_2               2               103
  CLUS_3               3                92
D17V9, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               4               154
  CLUS_2               7               176
  CLUS_3               1                56
D17V10, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               3               160
  CLUS_2               5               110
  CLUS_3               4               116

Clustering(18) Variable = 9q gain mutation analysis
D18V1, multiclass
D18V2, multiclass
D18V3, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               4               144
  CLUS_2               1               187
  CLUS_3               2                85
  CLUS_4               0                49
D18V4, multiclass
D18V5, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               0                85
  CLUS_2               2                73
  CLUS_3               2                73
D18V6, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               0                23
  CLUS_2               0                89
  CLUS_3               2                63
  CLUS_4               2                56
D18V7, multiclass
D18V8, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               3               149
  CLUS_2               0               105
  CLUS_3               2                93
D18V9, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2               156
  CLUS_2               3               180
  CLUS_3               2                55
D18V10, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1               162
  CLUS_2               3               112
  CLUS_3               3               117

Clustering(19) Variable = 10p gain mutation analysis
D19V1, multiclass
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1680         TCGA-67-3770 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-67-3774 
"10P GAIN WILD-TYPE" 
D19V2, multiclass
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1680         TCGA-67-3770 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-67-3774 
"10P GAIN WILD-TYPE" 
D19V3, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               19                129
  CLUS_2               11                177
  CLUS_3               11                 76
  CLUS_4                8                 41
D19V4, multiclass
D19V5, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                6                 79
  CLUS_2               11                 64
  CLUS_3               12                 63
D19V6, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                4                 19
  CLUS_2                6                 83
  CLUS_3               11                 54
  CLUS_4                8                 50
D19V7, multiclass
D19V8, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               15                137
  CLUS_2               15                 90
  CLUS_3                8                 87
D19V9, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               17                141
  CLUS_2               23                160
  CLUS_3                2                 55
D19V10, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               17                146
  CLUS_2               10                105
  CLUS_3               15                105

Clustering(20) Variable = 10q gain mutation analysis
D20V1, multiclass
D20V2, multiclass
D20V3, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                7                141
  CLUS_2                9                179
  CLUS_3                5                 82
  CLUS_4                7                 42
D20V4, multiclass
D20V5, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                4                 81
  CLUS_2                7                 68
  CLUS_3                5                 70
D20V6, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                2                 21
  CLUS_2                3                 86
  CLUS_3                4                 61
  CLUS_4                7                 51
D20V7, multiclass
D20V8, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               12                140
  CLUS_2                6                 99
  CLUS_3                2                 93
D20V9, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               11                147
  CLUS_2                9                174
  CLUS_3                3                 54
D20V10, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               13                150
  CLUS_2                3                112
  CLUS_3                7                113

Clustering(21) Variable = 11p gain mutation analysis
D21V1, multiclass
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1595 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-67-3774 
"11P GAIN WILD-TYPE" 
D21V2, multiclass
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1595 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-67-3774 
"11P GAIN WILD-TYPE" 
D21V3, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               13                135
  CLUS_2                7                181
  CLUS_3               10                 77
  CLUS_4                5                 44
D21V4, multiclass
D21V5, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                5                 80
  CLUS_2                3                 72
  CLUS_3               10                 65
D21V6, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                 23
  CLUS_2                7                 82
  CLUS_3                7                 58
  CLUS_4                4                 54
D21V7, multiclass
D21V8, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                9                143
  CLUS_2               13                 92
  CLUS_3                6                 89
D21V9, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                7                151
  CLUS_2               17                166
  CLUS_3                7                 50
D21V10, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                7                156
  CLUS_2               10                105
  CLUS_3               14                106

Clustering(22) Variable = 11q gain mutation analysis
D22V1, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                  5
  CLUS_2                1                  8
  CLUS_3                0                 12
  CLUS_4                2                  4
D22V2, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                2                  5
  CLUS_2                1                 12
  CLUS_3                0                 12
D22V3, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               23                125
  CLUS_2                8                180
  CLUS_3               14                 73
  CLUS_4                6                 43
D22V4, multiclass
D22V5, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                8                 77
  CLUS_2                3                 72
  CLUS_3               18                 57
D22V6, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                 23
  CLUS_2               11                 78
  CLUS_3               14                 51
  CLUS_4                4                 54
D22V7, multiclass
D22V8, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                8                144
  CLUS_2               20                 85
  CLUS_3               13                 82
D22V9, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                8                150
  CLUS_2               27                156
  CLUS_3               10                 47
D22V10, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                9                154
  CLUS_2               19                 96
  CLUS_3               17                103

Clustering(23) Variable = 12p gain mutation analysis
D23V1, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                  4
  CLUS_2                1                  8
  CLUS_3                1                 11
  CLUS_4                2                  4
D23V2, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                3                  4
  CLUS_2                1                 12
  CLUS_3                1                 11
D23V3, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               16                132
  CLUS_2                3                185
  CLUS_3               32                 55
  CLUS_4                6                 43
D23V4, multiclass
D23V5, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               12                 73
  CLUS_2                5                 70
  CLUS_3               12                 63
D23V6, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                0                 23
  CLUS_2               11                 78
  CLUS_3               12                 53
  CLUS_4                6                 52
D23V7, multiclass
D23V8, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                9                143
  CLUS_2               23                 82
  CLUS_3               12                 83
D23V9, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               10                148
  CLUS_2               32                151
  CLUS_3                7                 50
D23V10, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               11                152
  CLUS_2               15                100
  CLUS_3               23                 97

Clustering(24) Variable = 12q gain mutation analysis
D24V1, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                  4
  CLUS_2                1                  8
  CLUS_3                1                 11
  CLUS_4                2                  4
D24V2, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                3                  4
  CLUS_2                1                 12
  CLUS_3                1                 11
D24V3, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                9                139
  CLUS_2                3                185
  CLUS_3               27                 60
  CLUS_4                7                 42
D24V4, multiclass
D24V5, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                8                 77
  CLUS_2                4                 71
  CLUS_3               11                 64
D24V6, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                0                 23
  CLUS_2                8                 81
  CLUS_3               11                 54
  CLUS_4                4                 54
D24V7, multiclass
D24V8, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                8                144
  CLUS_2               19                 86
  CLUS_3                9                 86
D24V9, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                8                150
  CLUS_2               25                158
  CLUS_3                6                 51
D24V10, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                9                154
  CLUS_2                9                106
  CLUS_3               21                 99

Clustering(25) Variable = 13q gain mutation analysis
D25V1, multiclass
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1678         TCGA-67-3770 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-67-3772         TCGA-67-3773         TCGA-67-3774 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D25V2, multiclass
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1678         TCGA-67-3770 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-67-3772         TCGA-67-3773         TCGA-67-3774 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D25V3, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                145
  CLUS_2                5                183
  CLUS_3                6                 81
  CLUS_4                1                 48
D25V4, multiclass
D25V5, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                2                 83
  CLUS_2                3                 72
  CLUS_3                5                 70
D25V6, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                0                 23
  CLUS_2                2                 87
  CLUS_3                5                 60
  CLUS_4                3                 55
D25V7, multiclass
D25V8, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                6                146
  CLUS_2                7                 98
  CLUS_3                1                 94
D25V9, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                6                152
  CLUS_2                7                176
  CLUS_3                0                 57
D25V10, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                6                157
  CLUS_2                3                112
  CLUS_3                4                116

Clustering(26) Variable = 14q gain mutation analysis
D26V1, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-44-2661         TCGA-44-2662         TCGA-44-2665 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-44-2666         TCGA-44-2668         TCGA-44-3398 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-44-3918         TCGA-44-3919         TCGA-44-4112 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-55-1592         TCGA-55-1594         TCGA-55-1595 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"14Q GAIN WILD-TYPE" 
D26V2, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-44-2661         TCGA-44-2662         TCGA-44-2665 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-44-2666         TCGA-44-2668         TCGA-44-3398 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-44-3918         TCGA-44-3919         TCGA-44-4112 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-55-1592         TCGA-55-1594         TCGA-55-1595 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"14Q GAIN WILD-TYPE" 
D26V3, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               19                129
  CLUS_2                9                179
  CLUS_3               12                 75
  CLUS_4               16                 33
D26V4, multiclass
D26V5, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                8                 77
  CLUS_2                8                 67
  CLUS_3               15                 60
D26V6, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                2                 21
  CLUS_2               13                 76
  CLUS_3               11                 54
  CLUS_4                5                 53
D26V7, multiclass
D26V8, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               14                138
  CLUS_2               22                 83
  CLUS_3                7                 88
D26V9, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               11                147
  CLUS_2               32                151
  CLUS_3                7                 50
D26V10, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               11                152
  CLUS_2               16                 99
  CLUS_3               23                 97

Clustering(27) Variable = 15q gain mutation analysis
D27V1, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1595 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"15Q GAIN WILD-TYPE" 
D27V2, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1595 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"15Q GAIN WILD-TYPE" 
D27V3, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                5                143
  CLUS_2                3                185
  CLUS_3                5                 82
  CLUS_4                1                 48
D27V4, multiclass
D27V5, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                2                 83
  CLUS_2                3                 72
  CLUS_3                3                 72
D27V6, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                0                 23
  CLUS_2                4                 85
  CLUS_3                1                 64
  CLUS_4                3                 55
D27V7, multiclass
D27V8, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                7                145
  CLUS_2                4                101
  CLUS_3                1                 94
D27V9, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                6                152
  CLUS_2                6                177
  CLUS_3                1                 56
D27V10, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                8                155
  CLUS_2                2                113
  CLUS_3                3                117

Clustering(28) Variable = 16p gain mutation analysis
D28V1, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                  3
  CLUS_2                1                  8
  CLUS_3                2                 10
  CLUS_4                0                  6
D28V2, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                2                 11
  CLUS_3                3                  9
D28V3, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               27                121
  CLUS_2               22                166
  CLUS_3               13                 74
  CLUS_4                5                 44
D28V4, multiclass
D28V5, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               17                 68
  CLUS_2                6                 69
  CLUS_3                9                 66
D28V6, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                3                 20
  CLUS_2               16                 73
  CLUS_3                8                 57
  CLUS_4                5                 53
D28V7, multiclass
D28V8, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               27                125
  CLUS_2                8                 97
  CLUS_3               16                 79
D28V9, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               27                131
  CLUS_2               18                165
  CLUS_3               14                 43
D28V10, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               31                132
  CLUS_2               18                 97
  CLUS_3               10                110

Clustering(29) Variable = 16q gain mutation analysis
D29V1, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                  4
  CLUS_2                2                  7
  CLUS_3                0                 12
  CLUS_4                0                  6
D29V2, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                0                 13
  CLUS_3                3                  9
D29V3, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               17                131
  CLUS_2               13                175
  CLUS_3                9                 78
  CLUS_4                3                 46
D29V4, multiclass
D29V5, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               12                 73
  CLUS_2                2                 73
  CLUS_3                9                 66
D29V6, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                 22
  CLUS_2               14                 75
  CLUS_3                7                 58
  CLUS_4                1                 57
D29V7, multiclass
D29V8, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               16                136
  CLUS_2                6                 99
  CLUS_3               12                 83
D29V9, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               17                141
  CLUS_2               13                170
  CLUS_3                9                 48
D29V10, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               20                143
  CLUS_2               16                 99
  CLUS_3                3                117

Clustering(30) Variable = 17p gain mutation analysis
D30V1, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1678         TCGA-67-3770 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-67-3774 
"17P GAIN WILD-TYPE" 
D30V2, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1678         TCGA-67-3770 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-67-3774 
"17P GAIN WILD-TYPE" 
D30V3, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                5                143
  CLUS_2                3                185
  CLUS_3               13                 74
  CLUS_4                7                 42
D30V4, multiclass
D30V5, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                5                 80
  CLUS_2                2                 73
  CLUS_3                3                 72
D30V6, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                1                 22
  CLUS_2                2                 87
  CLUS_3                3                 62
  CLUS_4                4                 54
D30V7, multiclass
D30V8, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                8                144
  CLUS_2                7                 98
  CLUS_3                6                 89
D30V9, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                8                150
  CLUS_2               16                167
  CLUS_3                1                 56
D30V10, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                9                154
  CLUS_2                6                109
  CLUS_3               10                110

Clustering(31) Variable = 17q gain mutation analysis
D31V1, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                3                  2
  CLUS_2                1                  8
  CLUS_3                1                 11
  CLUS_4                0                  6
D31V2, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                1                 12
  CLUS_3                3                  9
D31V3, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               37                111
  CLUS_2                9                179
  CLUS_3               22                 65
  CLUS_4               10                 39
D31V4, multiclass
D31V5, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               15                 70
  CLUS_2                8                 67
  CLUS_3               13                 62
D31V6, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                 22
  CLUS_2               16                 73
  CLUS_3               13                 52
  CLUS_4                6                 52
D31V7, multiclass
D31V8, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               21                131
  CLUS_2               14                 91
  CLUS_3               24                 71
D31V9, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               20                138
  CLUS_2               41                142
  CLUS_3                9                 48
D31V10, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               21                142
  CLUS_2               21                 94
  CLUS_3               28                 92

Clustering(32) Variable = 18p gain mutation analysis
D32V1, multiclass
D32V2, multiclass
D32V3, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               22                126
  CLUS_2                5                183
  CLUS_3                4                 83
  CLUS_4               11                 38
D32V4, multiclass
D32V5, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                3                 82
  CLUS_2               10                 65
  CLUS_3                6                 69
D32V6, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                 22
  CLUS_2                4                 85
  CLUS_3                6                 59
  CLUS_4                8                 50
D32V7, multiclass
D32V8, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                8                144
  CLUS_2               14                 91
  CLUS_3               10                 85
D32V9, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                9                149
  CLUS_2               25                158
  CLUS_3                3                 54
D32V10, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                9                154
  CLUS_2               10                105
  CLUS_3               18                102

Clustering(33) Variable = 18q gain mutation analysis
D33V1, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1680         TCGA-67-3770 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"18Q GAIN WILD-TYPE" 
D33V2, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1680         TCGA-67-3770 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"18Q GAIN WILD-TYPE" 
D33V3, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               12                136
  CLUS_2                2                186
  CLUS_3                3                 84
  CLUS_4                9                 40
D33V4, multiclass
D33V5, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                 83
  CLUS_2                4                 71
  CLUS_3                8                 67
D33V6, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                 22
  CLUS_2                1                 88
  CLUS_3                7                 58
  CLUS_4                5                 53
D33V7, multiclass
D33V8, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                3                149
  CLUS_2               12                 93
  CLUS_3                5                 90
D33V9, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                5                153
  CLUS_2               16                167
  CLUS_3                3                 54
D33V10, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                5                158
  CLUS_2                5                110
  CLUS_3               14                106

Clustering(34) Variable = 19p gain mutation analysis
D34V1, multiclass
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2666 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-44-2668         TCGA-44-3398         TCGA-44-3918 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-44-3919         TCGA-44-4112         TCGA-55-1592 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-55-1594         TCGA-55-1595         TCGA-55-1596 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-64-1676         TCGA-64-1677         TCGA-64-1678 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-64-1680         TCGA-67-3770         TCGA-67-3771 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-67-3772         TCGA-67-3773         TCGA-67-3774 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
D34V2, multiclass
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2666 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-44-2668         TCGA-44-3398         TCGA-44-3918 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-44-3919         TCGA-44-4112         TCGA-55-1592 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-55-1594         TCGA-55-1595         TCGA-55-1596 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-64-1676         TCGA-64-1677         TCGA-64-1678 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-64-1680         TCGA-67-3770         TCGA-67-3771 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-67-3772         TCGA-67-3773         TCGA-67-3774 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
D34V3, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                147
  CLUS_2                3                185
  CLUS_3                1                 86
  CLUS_4                1                 48
D34V4, multiclass
D34V5, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                2                 83
  CLUS_2                0                 75
  CLUS_3                1                 74
D34V6, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                 23
  CLUS_2                1                 88
  CLUS_3                1                 64
  CLUS_4                1                 57
D34V7, multiclass
D34V8, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                3                149
  CLUS_2                1                104
  CLUS_3                1                 94
D34V9, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                157
  CLUS_2                3                180
  CLUS_3                2                 55
D34V10, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                2                161
  CLUS_2                3                112
  CLUS_3                1                119

Clustering(35) Variable = 19q gain mutation analysis
D35V1, multiclass
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2665 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-44-2666         TCGA-44-2668         TCGA-44-3398 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-44-3918         TCGA-44-3919         TCGA-44-4112 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-55-1592         TCGA-55-1594         TCGA-55-1595 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"19Q GAIN WILD-TYPE" 
D35V2, multiclass
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2665 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-44-2666         TCGA-44-2668         TCGA-44-3398 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-44-3918         TCGA-44-3919         TCGA-44-4112 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-55-1592         TCGA-55-1594         TCGA-55-1595 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"19Q GAIN WILD-TYPE" 
D35V3, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                3                145
  CLUS_2                4                184
  CLUS_3                8                 79
  CLUS_4                7                 42
D35V4, multiclass
D35V5, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                 83
  CLUS_2                2                 73
  CLUS_3                5                 70
D35V6, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                 21
  CLUS_2                0                 89
  CLUS_3                5                 60
  CLUS_4                2                 56
D35V7, multiclass
D35V8, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                7                145
  CLUS_2                6                 99
  CLUS_3                3                 92
D35V9, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                3                155
  CLUS_2               15                168
  CLUS_3                2                 55
D35V10, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                4                159
  CLUS_2                9                106
  CLUS_3                7                113

Clustering(36) Variable = 20p gain mutation analysis
D36V1, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                0                  5
  CLUS_2                1                  8
  CLUS_3                0                 12
  CLUS_4                3                  3
D36V2, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                3                  4
  CLUS_2                0                 13
  CLUS_3                1                 11
D36V3, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               15                133
  CLUS_2               11                177
  CLUS_3               22                 65
  CLUS_4               13                 36
D36V4, multiclass
D36V5, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                9                 76
  CLUS_2                7                 68
  CLUS_3               18                 57
D36V6, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                2                 21
  CLUS_2               13                 76
  CLUS_3               12                 53
  CLUS_4                7                 51
D36V7, multiclass
D36V8, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               14                138
  CLUS_2               26                 79
  CLUS_3                8                 87
D36V9, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               15                143
  CLUS_2               33                150
  CLUS_3                7                 50
D36V10, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               15                148
  CLUS_2               15                100
  CLUS_3               25                 95

Clustering(37) Variable = 20q gain mutation analysis
D37V1, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                0                  5
  CLUS_2                1                  8
  CLUS_3                0                 12
  CLUS_4                4                  2
D37V2, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                4                  3
  CLUS_2                0                 13
  CLUS_3                1                 11
D37V3, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               27                121
  CLUS_2               11                177
  CLUS_3               26                 61
  CLUS_4               12                 37
D37V4, multiclass
D37V5, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               11                 74
  CLUS_2                9                 66
  CLUS_3               25                 50
D37V6, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                3                 20
  CLUS_2               18                 71
  CLUS_3               18                 47
  CLUS_4                6                 52
D37V7, multiclass
D37V8, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               21                131
  CLUS_2               31                 74
  CLUS_3               11                 84
D37V9, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               17                141
  CLUS_2               44                139
  CLUS_3                9                 48
D37V10, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               18                145
  CLUS_2               23                 92
  CLUS_3               29                 91

Clustering(38) Variable = 21q gain mutation analysis
D38V1, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                  5
  CLUS_2                0                  9
  CLUS_3                1                 11
  CLUS_4                2                  4
D38V2, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                2                  5
  CLUS_2                1                 12
  CLUS_3                0                 12
D38V3, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               27                121
  CLUS_2                8                180
  CLUS_3                4                 83
  CLUS_4                2                 47
D38V4, multiclass
D38V5, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               12                 73
  CLUS_2                3                 72
  CLUS_3                7                 68
D38V6, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                2                 21
  CLUS_2               13                 76
  CLUS_3                6                 59
  CLUS_4                1                 57
D38V7, multiclass
D38V8, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               15                137
  CLUS_2                4                101
  CLUS_3               12                 83
D38V9, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               11                147
  CLUS_2               20                163
  CLUS_3                4                 53
D38V10, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               11                152
  CLUS_2               13                102
  CLUS_3               11                109

Clustering(39) Variable = 22q gain mutation analysis
D39V1, multiclass
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1594         TCGA-55-1595 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"22Q GAIN WILD-TYPE" 
D39V2, multiclass
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1594         TCGA-55-1595 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"22Q GAIN WILD-TYPE" 
D39V3, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                8                140
  CLUS_2                3                185
  CLUS_3                5                 82
  CLUS_4                4                 45
D39V4, multiclass
D39V5, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                4                 81
  CLUS_2                2                 73
  CLUS_3                4                 71
D39V6, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                2                 21
  CLUS_2                2                 87
  CLUS_3                5                 60
  CLUS_4                1                 57
D39V7, multiclass
D39V8, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                6                146
  CLUS_2                6                 99
  CLUS_3                4                 91
D39V9, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                3                155
  CLUS_2               10                173
  CLUS_3                6                 51
D39V10, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                4                159
  CLUS_2                7                108
  CLUS_3                8                112

Clustering(40) Variable = Xq gain mutation analysis
D40V1, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                 4
  CLUS_2               1                 8
  CLUS_3               1                11
  CLUS_4               0                 6
D40V2, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               1                12
  CLUS_3               2                10
D40V3, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              10               138
  CLUS_2               0               188
  CLUS_3               6                81
  CLUS_4               3                46
D40V4, multiclass
D40V5, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               2                83
  CLUS_2               3                72
  CLUS_3               5                70
D40V6, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                23
  CLUS_2               6                83
  CLUS_3               2                63
  CLUS_4               2                56
D40V7, multiclass
D40V8, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               6               146
  CLUS_2               5               100
  CLUS_3               7                88
D40V9, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               5               153
  CLUS_2              10               173
  CLUS_3               4                53
D40V10, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               4               159
  CLUS_2               7               108
  CLUS_3               8               112

Clustering(41) Variable = 1p loss mutation analysis
D41V1, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-35-3615        TCGA-35-4122 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-35-4123        TCGA-44-2655        TCGA-44-2656        TCGA-44-2657 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-44-2659        TCGA-44-2661        TCGA-44-2662        TCGA-44-2665 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-44-2666        TCGA-44-2668        TCGA-44-3398        TCGA-44-3918 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-44-3919        TCGA-44-4112        TCGA-55-1592        TCGA-55-1594 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-55-1595        TCGA-55-1596        TCGA-64-1676        TCGA-64-1677 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D41V2, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-35-3615        TCGA-35-4122 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-35-4123        TCGA-44-2655        TCGA-44-2656        TCGA-44-2657 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-44-2659        TCGA-44-2661        TCGA-44-2662        TCGA-44-2665 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-44-2666        TCGA-44-2668        TCGA-44-3398        TCGA-44-3918 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-44-3919        TCGA-44-4112        TCGA-55-1592        TCGA-55-1594 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-55-1595        TCGA-55-1596        TCGA-64-1676        TCGA-64-1677 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D41V3, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               5               143
  CLUS_2               7               181
  CLUS_3               8                79
  CLUS_4               8                41
D41V4, multiclass
D41V5, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               4                81
  CLUS_2               4                71
  CLUS_3              10                65
D41V6, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                22
  CLUS_2               4                85
  CLUS_3               9                56
  CLUS_4               4                54
D41V7, multiclass
D41V8, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               6               146
  CLUS_2              11                94
  CLUS_3               6                89
D41V9, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               9               149
  CLUS_2              15               168
  CLUS_3               2                55
D41V10, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               8               155
  CLUS_2               8               107
  CLUS_3              10               110

Clustering(42) Variable = 1q loss mutation analysis
D42V1, multiclass
D42V2, multiclass
D42V3, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               2               146
  CLUS_2               2               186
  CLUS_3               4                83
  CLUS_4               3                46
D42V4, multiclass
D42V5, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               2                83
  CLUS_2               1                74
  CLUS_3               5                70
D42V6, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               1                22
  CLUS_2               1                88
  CLUS_3               6                59
  CLUS_4               0                58
D42V7, multiclass
D42V8, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               1               151
  CLUS_2               5               100
  CLUS_3               3                92
D42V9, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               2               156
  CLUS_2               8               175
  CLUS_3               1                56
D42V10, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               2               161
  CLUS_2               4               111
  CLUS_3               5               115

Clustering(43) Variable = 2p loss mutation analysis
D43V1, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-44-2666        TCGA-44-2668        TCGA-44-3398        TCGA-44-3918 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-44-3919        TCGA-44-4112        TCGA-55-1592        TCGA-55-1594 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-55-1595        TCGA-55-1596        TCGA-64-1676        TCGA-64-1677 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D43V2, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-44-2666        TCGA-44-2668        TCGA-44-3398        TCGA-44-3918 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-44-3919        TCGA-44-4112        TCGA-55-1592        TCGA-55-1594 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-55-1595        TCGA-55-1596        TCGA-64-1676        TCGA-64-1677 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D43V3, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               2               146
  CLUS_2               2               186
  CLUS_3               1                86
  CLUS_4               1                48
D43V4, multiclass
D43V5, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               1                84
  CLUS_2               1                74
  CLUS_3               1                74
D43V6, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0                23
  CLUS_2               1                88
  CLUS_3               2                63
  CLUS_4               0                58
D43V7, multiclass
D43V8, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               2               150
  CLUS_2               2               103
  CLUS_3               0                95
D43V9, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               3               155
  CLUS_2               1               182
  CLUS_3               1                56
D43V10, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               2               161
  CLUS_2               1               114
  CLUS_3               2               118

Clustering(44) Variable = 2q loss mutation analysis
D44V1, multiclass
D44V2, multiclass
D44V3, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               2               146
  CLUS_2               0               188
  CLUS_3               2                85
  CLUS_4               0                49
D44V4, multiclass
D44V5, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2               233 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-05-4384 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4396        TCGA-05-4397        TCGA-05-4398        TCGA-05-4402 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4405        TCGA-05-4410        TCGA-05-4417        TCGA-05-4418 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4420        TCGA-05-4422        TCGA-05-4426        TCGA-05-4427 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4430        TCGA-05-4434        TCGA-05-5420        TCGA-05-5423 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-5425        TCGA-05-5429        TCGA-05-5715        TCGA-35-3615 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-38-4625 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-38-4626        TCGA-38-4627        TCGA-38-4629        TCGA-38-6178 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-2656        TCGA-44-2657        TCGA-44-2661        TCGA-44-2665 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-2668        TCGA-44-3396        TCGA-44-3398        TCGA-44-3918 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-3919        TCGA-44-4112        TCGA-44-5643        TCGA-44-5644 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-5645        TCGA-44-6144        TCGA-44-6145        TCGA-44-6146 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-6147        TCGA-44-6148        TCGA-44-6774        TCGA-44-6775 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-6776        TCGA-44-6777        TCGA-44-6778        TCGA-44-6779 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-7659        TCGA-44-7660        TCGA-44-7661        TCGA-44-7662 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-7667        TCGA-44-7669        TCGA-44-7670        TCGA-44-7671 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-7672        TCGA-49-4486        TCGA-49-4487        TCGA-49-4488 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-4494        TCGA-49-4501        TCGA-49-4505        TCGA-49-4506 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-4507        TCGA-49-4510        TCGA-49-4512        TCGA-49-4514 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-6742        TCGA-49-6743        TCGA-49-6744        TCGA-49-6745 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-6761        TCGA-49-6767        TCGA-50-5044        TCGA-50-5045 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5049        TCGA-50-5051        TCGA-50-5066        TCGA-50-5068 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5072        TCGA-50-5930        TCGA-50-5931        TCGA-50-5932 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5933        TCGA-50-5936        TCGA-50-5939        TCGA-50-5941 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5942        TCGA-50-5944        TCGA-50-5946        TCGA-50-6590 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-6591        TCGA-50-6592        TCGA-50-6593        TCGA-50-6594 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-6595        TCGA-50-6597        TCGA-50-6673        TCGA-50-7109 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-53-7624        TCGA-53-7626        TCGA-53-7813        TCGA-55-1592 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1596        TCGA-55-5899        TCGA-55-6543 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-6712        TCGA-55-6969        TCGA-55-6970        TCGA-55-6971 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-6978        TCGA-55-6979        TCGA-55-6981        TCGA-55-6982 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-7573        TCGA-55-7574        TCGA-55-7728        TCGA-55-7815 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-7910        TCGA-55-7911        TCGA-64-1676        TCGA-64-1677 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1679        TCGA-64-1680        TCGA-64-1681 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-64-5774        TCGA-64-5778        TCGA-64-5779        TCGA-64-5781 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-64-5815        TCGA-67-3771        TCGA-67-6215        TCGA-67-6216 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-67-6217        TCGA-69-7761        TCGA-69-7763        TCGA-69-7764 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-69-7765        TCGA-71-6725        TCGA-73-4658        TCGA-73-4659 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-73-4670        TCGA-73-4675        TCGA-73-4676        TCGA-73-7498 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-73-7499        TCGA-75-5122        TCGA-75-5125        TCGA-75-6203 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-75-6205        TCGA-75-6206        TCGA-75-6207        TCGA-75-6212 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-75-6214        TCGA-75-7027        TCGA-75-7030        TCGA-75-7031 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7143        TCGA-78-7145        TCGA-78-7146        TCGA-78-7147 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7148        TCGA-78-7149        TCGA-78-7150        TCGA-78-7152 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7153        TCGA-78-7154        TCGA-78-7155        TCGA-78-7156 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7158        TCGA-78-7159        TCGA-78-7160        TCGA-78-7161 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7162        TCGA-78-7163        TCGA-78-7166        TCGA-78-7167 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7535        TCGA-78-7536        TCGA-78-7537        TCGA-78-7539 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7540        TCGA-78-7542        TCGA-78-7633        TCGA-80-5607 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-80-5608        TCGA-80-5611        TCGA-83-5908        TCGA-86-6562 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-86-6851        TCGA-86-7701        TCGA-86-7711        TCGA-86-7713 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-86-7953        TCGA-86-7954        TCGA-86-7955        TCGA-91-6828 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-91-6829        TCGA-91-6830        TCGA-91-6831        TCGA-91-6835 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-91-6836        TCGA-91-6840        TCGA-91-6847        TCGA-91-6848 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-91-6849        TCGA-91-7771        TCGA-93-7348        TCGA-95-7039 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-95-7043        TCGA-95-7567        TCGA-95-7944        TCGA-95-7947 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-95-7948        TCGA-97-7546        TCGA-97-7552        TCGA-97-7553 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-97-7554        TCGA-97-7937        TCGA-97-7938        TCGA-97-7941 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-99-7458 
"2Q LOSS WILD-TYPE" 
D44V6, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2               233 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-05-4384 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4396        TCGA-05-4397        TCGA-05-4398        TCGA-05-4402 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4405        TCGA-05-4410        TCGA-05-4417        TCGA-05-4418 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4420        TCGA-05-4422        TCGA-05-4426        TCGA-05-4427 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4430        TCGA-05-4434        TCGA-05-5420        TCGA-05-5423 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-5425        TCGA-05-5429        TCGA-05-5715        TCGA-35-3615 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-38-4625 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-38-4626        TCGA-38-4627        TCGA-38-4629        TCGA-38-6178 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-2656        TCGA-44-2657        TCGA-44-2661        TCGA-44-2665 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-2668        TCGA-44-3396        TCGA-44-3398        TCGA-44-3918 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-3919        TCGA-44-4112        TCGA-44-5643        TCGA-44-5644 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-5645        TCGA-44-6144        TCGA-44-6145        TCGA-44-6146 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-6147        TCGA-44-6148        TCGA-44-6774        TCGA-44-6775 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-6776        TCGA-44-6777        TCGA-44-6778        TCGA-44-6779 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-7659        TCGA-44-7660        TCGA-44-7661        TCGA-44-7662 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-7667        TCGA-44-7669        TCGA-44-7670        TCGA-44-7671 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-7672        TCGA-49-4486        TCGA-49-4487        TCGA-49-4488 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-4494        TCGA-49-4501        TCGA-49-4505        TCGA-49-4506 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-4507        TCGA-49-4510        TCGA-49-4512        TCGA-49-4514 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-6742        TCGA-49-6743        TCGA-49-6744        TCGA-49-6745 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-6761        TCGA-49-6767        TCGA-50-5044        TCGA-50-5045 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5049        TCGA-50-5051        TCGA-50-5066        TCGA-50-5068 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5072        TCGA-50-5930        TCGA-50-5931        TCGA-50-5932 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5933        TCGA-50-5936        TCGA-50-5939        TCGA-50-5941 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5942        TCGA-50-5944        TCGA-50-5946        TCGA-50-6590 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-6591        TCGA-50-6592        TCGA-50-6593        TCGA-50-6594 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-6595        TCGA-50-6597        TCGA-50-6673        TCGA-50-7109 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-53-7624        TCGA-53-7626        TCGA-53-7813        TCGA-55-1592 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1596        TCGA-55-5899        TCGA-55-6543 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-6712        TCGA-55-6969        TCGA-55-6970        TCGA-55-6971 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-6978        TCGA-55-6979        TCGA-55-6981        TCGA-55-6982 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-7573        TCGA-55-7574        TCGA-55-7728        TCGA-55-7815 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-7910        TCGA-55-7911        TCGA-64-1676        TCGA-64-1677 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1679        TCGA-64-1680        TCGA-64-1681 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-64-5774        TCGA-64-5778        TCGA-64-5779        TCGA-64-5781 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-64-5815        TCGA-67-3771        TCGA-67-6215        TCGA-67-6216 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-67-6217        TCGA-69-7761        TCGA-69-7763        TCGA-69-7764 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-69-7765        TCGA-71-6725        TCGA-73-4658        TCGA-73-4659 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-73-4670        TCGA-73-4675        TCGA-73-4676        TCGA-73-7498 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-73-7499        TCGA-75-5122        TCGA-75-5125        TCGA-75-6203 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-75-6205        TCGA-75-6206        TCGA-75-6207        TCGA-75-6212 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-75-6214        TCGA-75-7027        TCGA-75-7030        TCGA-75-7031 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7143        TCGA-78-7145        TCGA-78-7146        TCGA-78-7147 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7148        TCGA-78-7149        TCGA-78-7150        TCGA-78-7152 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7153        TCGA-78-7154        TCGA-78-7155        TCGA-78-7156 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7158        TCGA-78-7159        TCGA-78-7160        TCGA-78-7161 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7162        TCGA-78-7163        TCGA-78-7166        TCGA-78-7167 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7535        TCGA-78-7536        TCGA-78-7537        TCGA-78-7539 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7540        TCGA-78-7542        TCGA-78-7633        TCGA-80-5607 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-80-5608        TCGA-80-5611        TCGA-83-5908        TCGA-86-6562 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-86-6851        TCGA-86-7701        TCGA-86-7711        TCGA-86-7713 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-86-7953        TCGA-86-7954        TCGA-86-7955        TCGA-91-6828 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-91-6829        TCGA-91-6830        TCGA-91-6831        TCGA-91-6835 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-91-6836        TCGA-91-6840        TCGA-91-6847        TCGA-91-6848 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-91-6849        TCGA-91-7771        TCGA-93-7348        TCGA-95-7039 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-95-7043        TCGA-95-7567        TCGA-95-7944        TCGA-95-7947 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-95-7948        TCGA-97-7546        TCGA-97-7552        TCGA-97-7553 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-97-7554        TCGA-97-7937        TCGA-97-7938        TCGA-97-7941 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-99-7458 
"2Q LOSS WILD-TYPE" 
D44V7, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2               350 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-05-4382 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4384        TCGA-05-4389        TCGA-05-4390        TCGA-05-4395 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4396        TCGA-05-4397        TCGA-05-4398        TCGA-05-4402 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4403        TCGA-05-4405        TCGA-05-4410        TCGA-05-4415 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4417        TCGA-05-4418        TCGA-05-4420        TCGA-05-4422 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4424        TCGA-05-4425        TCGA-05-4426        TCGA-05-4427 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4430        TCGA-05-4432        TCGA-05-4433        TCGA-05-4434 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-5420        TCGA-05-5423        TCGA-05-5425        TCGA-05-5428 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-5429        TCGA-05-5715        TCGA-35-3615        TCGA-35-4122 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-35-4123        TCGA-35-5375        TCGA-38-4625        TCGA-38-4626 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-38-4627        TCGA-38-4628        TCGA-38-4629        TCGA-38-4630 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-38-4631        TCGA-38-4632        TCGA-38-6178        TCGA-38-7271 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-2655        TCGA-44-2656        TCGA-44-2657        TCGA-44-2659 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-2661        TCGA-44-2662        TCGA-44-2665        TCGA-44-2666 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-2668        TCGA-44-3396        TCGA-44-3398        TCGA-44-3918 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-3919        TCGA-44-4112        TCGA-44-5643        TCGA-44-5644 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-5645        TCGA-44-6145        TCGA-44-6146        TCGA-44-6147 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-6148        TCGA-44-6774        TCGA-44-6775        TCGA-44-6776 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-6777        TCGA-44-6778        TCGA-44-6779        TCGA-44-7659 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-7660        TCGA-44-7661        TCGA-44-7662        TCGA-44-7667 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-7669        TCGA-44-7670        TCGA-44-7671        TCGA-44-7672 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-8117        TCGA-44-8119        TCGA-44-8120        TCGA-49-4486 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-4487        TCGA-49-4488        TCGA-49-4490        TCGA-49-4494 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-4501        TCGA-49-4505        TCGA-49-4506        TCGA-49-4507 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-4510        TCGA-49-4512        TCGA-49-4514        TCGA-49-6742 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-6743        TCGA-49-6744        TCGA-49-6745        TCGA-49-6761 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-6767        TCGA-50-5044        TCGA-50-5049        TCGA-50-5051 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5055        TCGA-50-5066        TCGA-50-5068        TCGA-50-5072 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5931        TCGA-50-5932        TCGA-50-5933        TCGA-50-5935 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5936        TCGA-50-5939        TCGA-50-5941        TCGA-50-5942 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5944        TCGA-50-5946        TCGA-50-6590        TCGA-50-6591 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-6592        TCGA-50-6593        TCGA-50-6594        TCGA-50-6595 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-6597        TCGA-50-6673        TCGA-50-7109        TCGA-53-7624 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-53-7626        TCGA-53-7813        TCGA-55-1592        TCGA-55-1594 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-1595        TCGA-55-1596        TCGA-55-5899        TCGA-55-6543 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-6642        TCGA-55-6712        TCGA-55-6968        TCGA-55-6969 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-6970        TCGA-55-6971        TCGA-55-6972        TCGA-55-6975 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-6978        TCGA-55-6979        TCGA-55-6980        TCGA-55-6981 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-6982        TCGA-55-6983        TCGA-55-6984        TCGA-55-6985 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-6986        TCGA-55-6987        TCGA-55-7281        TCGA-55-7283 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-7284        TCGA-55-7570        TCGA-55-7573        TCGA-55-7574 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-7576        TCGA-55-7724        TCGA-55-7725        TCGA-55-7726 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-7727        TCGA-55-7728        TCGA-55-7815        TCGA-55-7903 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-7907        TCGA-55-7910        TCGA-55-7911        TCGA-55-7913 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-7914        TCGA-55-7994        TCGA-55-7995        TCGA-55-8085 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-8087        TCGA-55-8089        TCGA-55-8090        TCGA-55-8091 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-8092        TCGA-55-8094        TCGA-55-8096        TCGA-55-8097 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-8203        TCGA-55-8204        TCGA-55-8205        TCGA-55-8206 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-8207        TCGA-55-8208        TCGA-55-8299        TCGA-55-8301 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-64-1676        TCGA-64-1677        TCGA-64-1678        TCGA-64-1679 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-64-1680        TCGA-64-1681        TCGA-64-5774        TCGA-64-5775 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-64-5778        TCGA-64-5779        TCGA-64-5781        TCGA-64-5815 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-67-3770        TCGA-67-3771        TCGA-67-3772        TCGA-67-3773 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-67-3774        TCGA-67-4679        TCGA-67-6215        TCGA-67-6216 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-67-6217        TCGA-69-7761        TCGA-69-7763        TCGA-69-7764 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-69-7765        TCGA-69-7973        TCGA-69-7974        TCGA-69-7978 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-69-7979        TCGA-69-7980        TCGA-69-8253        TCGA-69-8254 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-69-8255        TCGA-71-6725        TCGA-73-4658        TCGA-73-4659 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-73-4662        TCGA-73-4666        TCGA-73-4668        TCGA-73-4670 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-73-4675        TCGA-73-4676        TCGA-73-4677        TCGA-73-7498 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-73-7499        TCGA-75-5122        TCGA-75-5125        TCGA-75-5126 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-75-5146        TCGA-75-5147        TCGA-75-6203        TCGA-75-6205 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-75-6206        TCGA-75-6207        TCGA-75-6212        TCGA-75-6214 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-75-7025        TCGA-75-7027        TCGA-75-7030        TCGA-75-7031 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7143        TCGA-78-7145        TCGA-78-7146        TCGA-78-7147 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7148        TCGA-78-7149        TCGA-78-7150        TCGA-78-7152 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7153        TCGA-78-7154        TCGA-78-7155        TCGA-78-7156 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7158        TCGA-78-7159        TCGA-78-7160        TCGA-78-7161 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7162        TCGA-78-7163        TCGA-78-7166        TCGA-78-7167 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7220        TCGA-78-7535        TCGA-78-7536        TCGA-78-7537 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7539        TCGA-78-7540        TCGA-78-7542        TCGA-78-7633 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-80-5607        TCGA-80-5608        TCGA-80-5611        TCGA-83-5908 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-86-6562        TCGA-86-6851        TCGA-86-7701        TCGA-86-7711 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-86-7713        TCGA-86-7714        TCGA-86-7953        TCGA-86-7954 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-86-7955        TCGA-86-8054        TCGA-86-8055        TCGA-86-8056 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-86-8073        TCGA-86-8074        TCGA-86-8075        TCGA-86-8076 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-86-8279        TCGA-86-8280        TCGA-86-8281        TCGA-91-6828 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-91-6829        TCGA-91-6830        TCGA-91-6831        TCGA-91-6835 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-91-6836        TCGA-91-6840        TCGA-91-6847        TCGA-91-6848 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-91-6849        TCGA-91-7771        TCGA-93-7347        TCGA-93-7348 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-93-8067        TCGA-95-7039        TCGA-95-7043        TCGA-95-7562 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-95-7567        TCGA-95-7944        TCGA-95-7947        TCGA-95-7948 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-95-8039        TCGA-97-7546        TCGA-97-7547        TCGA-97-7552 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-97-7553        TCGA-97-7554        TCGA-97-7937        TCGA-97-7938 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-97-7941        TCGA-97-8171        TCGA-97-8172        TCGA-97-8174 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-97-8175        TCGA-97-8177        TCGA-97-8179        TCGA-99-7458 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-99-8025        TCGA-99-8028        TCGA-99-8032        TCGA-99-8033 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-J2-8192        TCGA-J2-8194 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D44V8, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2               350 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-05-4382 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4384        TCGA-05-4389        TCGA-05-4390        TCGA-05-4395 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4396        TCGA-05-4397        TCGA-05-4398        TCGA-05-4402 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4403        TCGA-05-4405        TCGA-05-4410        TCGA-05-4415 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4417        TCGA-05-4418        TCGA-05-4420        TCGA-05-4422 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4424        TCGA-05-4425        TCGA-05-4426        TCGA-05-4427 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4430        TCGA-05-4432        TCGA-05-4433        TCGA-05-4434 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-5420        TCGA-05-5423        TCGA-05-5425        TCGA-05-5428 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-5429        TCGA-05-5715        TCGA-35-3615        TCGA-35-4122 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-35-4123        TCGA-35-5375        TCGA-38-4625        TCGA-38-4626 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-38-4627        TCGA-38-4628        TCGA-38-4629        TCGA-38-4630 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-38-4631        TCGA-38-4632        TCGA-38-6178        TCGA-38-7271 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-2655        TCGA-44-2656        TCGA-44-2657        TCGA-44-2659 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-2661        TCGA-44-2662        TCGA-44-2665        TCGA-44-2666 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-2668        TCGA-44-3396        TCGA-44-3398        TCGA-44-3918 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-3919        TCGA-44-4112        TCGA-44-5643        TCGA-44-5644 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-5645        TCGA-44-6145        TCGA-44-6146        TCGA-44-6147 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-6148        TCGA-44-6774        TCGA-44-6775        TCGA-44-6776 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-6777        TCGA-44-6778        TCGA-44-6779        TCGA-44-7659 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-7660        TCGA-44-7661        TCGA-44-7662        TCGA-44-7667 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-7669        TCGA-44-7670        TCGA-44-7671        TCGA-44-7672 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-8117        TCGA-44-8119        TCGA-44-8120        TCGA-49-4486 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-4487        TCGA-49-4488        TCGA-49-4490        TCGA-49-4494 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-4501        TCGA-49-4505        TCGA-49-4506        TCGA-49-4507 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-4510        TCGA-49-4512        TCGA-49-4514        TCGA-49-6742 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-6743        TCGA-49-6744        TCGA-49-6745        TCGA-49-6761 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-6767        TCGA-50-5044        TCGA-50-5049        TCGA-50-5051 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5055        TCGA-50-5066        TCGA-50-5068        TCGA-50-5072 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5931        TCGA-50-5932        TCGA-50-5933        TCGA-50-5935 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5936        TCGA-50-5939        TCGA-50-5941        TCGA-50-5942 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5944        TCGA-50-5946        TCGA-50-6590        TCGA-50-6591 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-6592        TCGA-50-6593        TCGA-50-6594        TCGA-50-6595 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-6597        TCGA-50-6673        TCGA-50-7109        TCGA-53-7624 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-53-7626        TCGA-53-7813        TCGA-55-1592        TCGA-55-1594 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-1595        TCGA-55-1596        TCGA-55-5899        TCGA-55-6543 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-6642        TCGA-55-6712        TCGA-55-6968        TCGA-55-6969 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-6970        TCGA-55-6971        TCGA-55-6972        TCGA-55-6975 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-6978        TCGA-55-6979        TCGA-55-6980        TCGA-55-6981 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-6982        TCGA-55-6983        TCGA-55-6984        TCGA-55-6985 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-6986        TCGA-55-6987        TCGA-55-7281        TCGA-55-7283 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-7284        TCGA-55-7570        TCGA-55-7573        TCGA-55-7574 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-7576        TCGA-55-7724        TCGA-55-7725        TCGA-55-7726 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-7727        TCGA-55-7728        TCGA-55-7815        TCGA-55-7903 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-7907        TCGA-55-7910        TCGA-55-7911        TCGA-55-7913 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-7914        TCGA-55-7994        TCGA-55-7995        TCGA-55-8085 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-8087        TCGA-55-8089        TCGA-55-8090        TCGA-55-8091 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-8092        TCGA-55-8094        TCGA-55-8096        TCGA-55-8097 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-8203        TCGA-55-8204        TCGA-55-8205        TCGA-55-8206 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-8207        TCGA-55-8208        TCGA-55-8299        TCGA-55-8301 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-64-1676        TCGA-64-1677        TCGA-64-1678        TCGA-64-1679 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-64-1680        TCGA-64-1681        TCGA-64-5774        TCGA-64-5775 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-64-5778        TCGA-64-5779        TCGA-64-5781        TCGA-64-5815 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-67-3770        TCGA-67-3771        TCGA-67-3772        TCGA-67-3773 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-67-3774        TCGA-67-4679        TCGA-67-6215        TCGA-67-6216 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-67-6217        TCGA-69-7761        TCGA-69-7763        TCGA-69-7764 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-69-7765        TCGA-69-7973        TCGA-69-7974        TCGA-69-7978 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-69-7979        TCGA-69-7980        TCGA-69-8253        TCGA-69-8254 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-69-8255        TCGA-71-6725        TCGA-73-4658        TCGA-73-4659 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-73-4662        TCGA-73-4666        TCGA-73-4668        TCGA-73-4670 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-73-4675        TCGA-73-4676        TCGA-73-4677        TCGA-73-7498 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-73-7499        TCGA-75-5122        TCGA-75-5125        TCGA-75-5126 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-75-5146        TCGA-75-5147        TCGA-75-6203        TCGA-75-6205 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-75-6206        TCGA-75-6207        TCGA-75-6212        TCGA-75-6214 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-75-7025        TCGA-75-7027        TCGA-75-7030        TCGA-75-7031 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7143        TCGA-78-7145        TCGA-78-7146        TCGA-78-7147 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7148        TCGA-78-7149        TCGA-78-7150        TCGA-78-7152 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7153        TCGA-78-7154        TCGA-78-7155        TCGA-78-7156 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7158        TCGA-78-7159        TCGA-78-7160        TCGA-78-7161 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7162        TCGA-78-7163        TCGA-78-7166        TCGA-78-7167 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7220        TCGA-78-7535        TCGA-78-7536        TCGA-78-7537 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7539        TCGA-78-7540        TCGA-78-7542        TCGA-78-7633 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-80-5607        TCGA-80-5608        TCGA-80-5611        TCGA-83-5908 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-86-6562        TCGA-86-6851        TCGA-86-7701        TCGA-86-7711 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-86-7713        TCGA-86-7714        TCGA-86-7953        TCGA-86-7954 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-86-7955        TCGA-86-8054        TCGA-86-8055        TCGA-86-8056 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-86-8073        TCGA-86-8074        TCGA-86-8075        TCGA-86-8076 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-86-8279        TCGA-86-8280        TCGA-86-8281        TCGA-91-6828 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-91-6829        TCGA-91-6830        TCGA-91-6831        TCGA-91-6835 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-91-6836        TCGA-91-6840        TCGA-91-6847        TCGA-91-6848 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-91-6849        TCGA-91-7771        TCGA-93-7347        TCGA-93-7348 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-93-8067        TCGA-95-7039        TCGA-95-7043        TCGA-95-7562 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-95-7567        TCGA-95-7944        TCGA-95-7947        TCGA-95-7948 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-95-8039        TCGA-97-7546        TCGA-97-7547        TCGA-97-7552 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-97-7553        TCGA-97-7554        TCGA-97-7937        TCGA-97-7938 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-97-7941        TCGA-97-8171        TCGA-97-8172        TCGA-97-8174 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-97-8175        TCGA-97-8177        TCGA-97-8179        TCGA-99-7458 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-99-8025        TCGA-99-8028        TCGA-99-8032        TCGA-99-8033 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-J2-8192        TCGA-J2-8194 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D44V9, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1               157
  CLUS_2               2               181
  CLUS_3               0                57
D44V10, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1               162
  CLUS_2               0               115
  CLUS_3               2               118

Clustering(45) Variable = 3p loss mutation analysis
D45V1, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               1                 8
  CLUS_3               2                10
  CLUS_4               3                 3
D45V2, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               3                 4
  CLUS_2               2                11
  CLUS_3               1                11
D45V3, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              32               116
  CLUS_2              21               167
  CLUS_3              26                61
  CLUS_4              14                35
D45V4, multiclass
D45V5, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              13                72
  CLUS_2              12                63
  CLUS_3              20                55
D45V6, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               4                19
  CLUS_2              19                70
  CLUS_3              15                50
  CLUS_4               7                51
D45V7, multiclass
D45V8, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              20               132
  CLUS_2              31                74
  CLUS_3              18                77
D45V9, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              22               136
  CLUS_2              47               136
  CLUS_3               7                50
D45V10, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              24               139
  CLUS_2              21                94
  CLUS_3              31                89

Clustering(46) Variable = 3q loss mutation analysis
D46V1, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               0                 9
  CLUS_3               2                10
  CLUS_4               1                 5
D46V2, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               2                11
  CLUS_3               0                12
D46V3, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              21               127
  CLUS_2              12               176
  CLUS_3              13                74
  CLUS_4              10                39
D46V4, multiclass
D46V5, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               5                80
  CLUS_2               9                66
  CLUS_3               9                66
D46V6, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               3                20
  CLUS_2               9                80
  CLUS_3               6                59
  CLUS_4               5                53
D46V7, multiclass
D46V8, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              15               137
  CLUS_2              17                88
  CLUS_3              10                85
D46V9, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              16               142
  CLUS_2              28               155
  CLUS_3               2                55
D46V10, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              17               146
  CLUS_2              12               103
  CLUS_3              17               103

Clustering(47) Variable = 4p loss mutation analysis
D47V1, multiclass
[1] "Remove cluster labels:" "4P LOSS MUTATED"       
clus
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1595        TCGA-64-1676        TCGA-64-1677 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
D47V2, multiclass
[1] "Remove cluster labels:" "4P LOSS MUTATED"       
clus
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1595        TCGA-64-1676        TCGA-64-1677 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
D47V3, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              12               136
  CLUS_2               4               184
  CLUS_3              11                76
  CLUS_4              11                38
D47V4, multiclass
D47V5, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               8                77
  CLUS_2               5                70
  CLUS_3              12                63
D47V6, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               2                21
  CLUS_2               6                83
  CLUS_3              11                54
  CLUS_4               6                52
D47V7, multiclass
D47V8, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               4               148
  CLUS_2              21                84
  CLUS_3               5                90
D47V9, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               6               152
  CLUS_2              25               158
  CLUS_3               2                55
D47V10, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               9               154
  CLUS_2               8               107
  CLUS_3              16               104

Clustering(48) Variable = 4q loss mutation analysis
D48V1, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               0                 9
  CLUS_3               0                12
  CLUS_4               3                 3
D48V2, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               3                 4
  CLUS_2               0                13
  CLUS_3               0                12
D48V3, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              15               133
  CLUS_2               1               187
  CLUS_3              17                70
  CLUS_4              12                37
D48V4, multiclass
D48V5, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               9                76
  CLUS_2               7                68
  CLUS_3              12                63
D48V6, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               2                21
  CLUS_2               9                80
  CLUS_3              11                54
  CLUS_4               6                52
D48V7, multiclass
D48V8, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               5               147
  CLUS_2              28                77
  CLUS_3               3                92
D48V9, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               7               151
  CLUS_2              28               155
  CLUS_3               3                54
D48V10, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               8               155
  CLUS_2               8               107
  CLUS_3              22                98

Clustering(49) Variable = 5p loss mutation analysis
D49V1, multiclass
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1595        TCGA-64-1676        TCGA-64-1677 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
D49V2, multiclass
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1595        TCGA-64-1676        TCGA-64-1677 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
D49V3, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               5               143
  CLUS_2               1               187
  CLUS_3               5                82
  CLUS_4               4                45
D49V4, multiclass
D49V5, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               1                84
  CLUS_2               2                73
  CLUS_3               4                71
D49V6, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               0                23
  CLUS_2               2                87
  CLUS_3               3                62
  CLUS_4               2                56
D49V7, multiclass
D49V8, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               2               150
  CLUS_2               8                97
  CLUS_3               4                91
D49V9, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               2               156
  CLUS_2              10               173
  CLUS_3               1                56
D49V10, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               1               162
  CLUS_2               6               109
  CLUS_3               6               114

Clustering(50) Variable = 5q loss mutation analysis
D50V1, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               1                 8
  CLUS_3               0                12
  CLUS_4               3                 3
D50V2, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               3                 4
  CLUS_2               0                13
  CLUS_3               1                11
D50V3, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              23               125
  CLUS_2               8               180
  CLUS_3              19                68
  CLUS_4               8                41
D50V4, multiclass
D50V5, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              11                74
  CLUS_2               6                69
  CLUS_3              17                58
D50V6, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               4                19
  CLUS_2              10                79
  CLUS_3              15                50
  CLUS_4               5                53
D50V7, multiclass
D50V8, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              11               141
  CLUS_2              20                85
  CLUS_3              16                79
D50V9, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              14               144
  CLUS_2              34               149
  CLUS_3               3                54
D50V10, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              14               149
  CLUS_2              15               100
  CLUS_3              22                98

Clustering(51) Variable = 6p loss mutation analysis
D51V1, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1                 4
  CLUS_2               1                 8
  CLUS_3               0                12
  CLUS_4               1                 5
D51V2, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               0                13
  CLUS_3               2                10
D51V3, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              15               133
  CLUS_2               8               180
  CLUS_3               7                80
  CLUS_4               8                41
D51V4, multiclass
D51V5, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               6                79
  CLUS_2               4                71
  CLUS_3              10                65
D51V6, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2                21
  CLUS_2               5                84
  CLUS_3               8                57
  CLUS_4               5                53
D51V7, multiclass
D51V8, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              12               140
  CLUS_2              10                95
  CLUS_3               9                86
D51V9, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              13               145
  CLUS_2              18               165
  CLUS_3               2                55
D51V10, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              15               148
  CLUS_2              10               105
  CLUS_3               8               112

Clustering(52) Variable = 6q loss mutation analysis
D52V1, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               1                 4
  CLUS_2               1                 8
  CLUS_3               2                10
  CLUS_4               2                 4
D52V2, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               2                 5
  CLUS_2               2                11
  CLUS_3               2                10
D52V3, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              36               112
  CLUS_2              33               155
  CLUS_3              19                68
  CLUS_4              17                32
D52V4, multiclass
D52V5, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              12                73
  CLUS_2              15                60
  CLUS_3              21                54
D52V6, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               2                21
  CLUS_2              12                77
  CLUS_3              17                48
  CLUS_4              17                41
D52V7, multiclass
D52V8, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              39               113
  CLUS_2              23                82
  CLUS_3              20                75
D52V9, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              37               121
  CLUS_2              45               138
  CLUS_3               8                49
D52V10, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              40               123
  CLUS_2              26                89
  CLUS_3              24                96

Clustering(53) Variable = 7p loss mutation analysis
D53V1, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               0                 9
  CLUS_3               2                10
  CLUS_4               1                 5
D53V2, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               2                11
  CLUS_3               0                12
D53V3, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               2               146
  CLUS_2               4               184
  CLUS_3               8                79
  CLUS_4               0                49
D53V4, multiclass
D53V5, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               1                84
  CLUS_2               2                73
  CLUS_3               3                72
D53V6, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0                23
  CLUS_2               2                87
  CLUS_3               2                63
  CLUS_4               2                56
D53V7, multiclass
D53V8, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               5               147
  CLUS_2               5               100
  CLUS_3               0                95
D53V9, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               5               153
  CLUS_2               6               177
  CLUS_3               1                56
D53V10, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               6               157
  CLUS_2               3               112
  CLUS_3               3               117

Clustering(54) Variable = 7q loss mutation analysis
D54V1, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               1                 4
  CLUS_2               0                 9
  CLUS_3               2                10
  CLUS_4               1                 5
D54V2, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               2                 5
  CLUS_2               2                11
  CLUS_3               0                12
D54V3, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               2               146
  CLUS_2               8               180
  CLUS_3               7                80
  CLUS_4               0                49
D54V4, multiclass
D54V5, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               2                83
  CLUS_2               1                74
  CLUS_3               3                72
D54V6, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               1                22
  CLUS_2               2                87
  CLUS_3               2                63
  CLUS_4               1                57
D54V7, multiclass
D54V8, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               4               148
  CLUS_2               6                99
  CLUS_3               1                94
D54V9, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               4               154
  CLUS_2               7               176
  CLUS_3               2                55
D54V10, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               4               159
  CLUS_2               4               111
  CLUS_3               5               115

Clustering(55) Variable = 8p loss mutation analysis
D55V1, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               4                 1
  CLUS_2               3                 6
  CLUS_3               2                10
  CLUS_4               2                 4
D55V2, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               3                 4
  CLUS_2               2                11
  CLUS_3               6                 6
D55V3, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              69                79
  CLUS_2              18               170
  CLUS_3              24                63
  CLUS_4               7                42
D55V4, multiclass
D55V5, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              23                62
  CLUS_2              14                61
  CLUS_3              24                51
D55V6, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               9                14
  CLUS_2              22                67
  CLUS_3              22                43
  CLUS_4               8                50
D55V7, multiclass
D55V8, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              34               118
  CLUS_2              26                79
  CLUS_3              36                59
D55V9, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              35               123
  CLUS_2              58               125
  CLUS_3              11                46
D55V10, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              31               132
  CLUS_2              36                79
  CLUS_3              37                83

Clustering(56) Variable = 8q loss mutation analysis
D56V1, multiclass
D56V2, multiclass
D56V3, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              13               135
  CLUS_2               4               184
  CLUS_3               0                87
  CLUS_4               0                49
D56V4, multiclass
D56V5, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               7                78
  CLUS_2               0                75
  CLUS_3               0                75
D56V6, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               3                20
  CLUS_2               4                85
  CLUS_3               0                65
  CLUS_4               0                58
D56V7, multiclass
D56V8, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               4               148
  CLUS_2               1               104
  CLUS_3               7                88
D56V9, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               6               152
  CLUS_2               6               177
  CLUS_3               3                54
D56V10, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               6               157
  CLUS_2               3               112
  CLUS_3               6               114

Clustering(57) Variable = 9p loss mutation analysis
D57V1, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                 4
  CLUS_2               1                 8
  CLUS_3               4                 8
  CLUS_4               4                 2
D57V2, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               4                 3
  CLUS_2               4                 9
  CLUS_3               2                10
D57V3, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              50                98
  CLUS_2              35               153
  CLUS_3              46                41
  CLUS_4               8                41
D57V4, multiclass
D57V5, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              23                62
  CLUS_2              22                53
  CLUS_3              28                47
D57V6, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               3                20
  CLUS_2              23                66
  CLUS_3              26                39
  CLUS_4              21                37
D57V7, multiclass
D57V8, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              41               111
  CLUS_2              45                60
  CLUS_3              23                72
D57V9, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              48               110
  CLUS_2              58               125
  CLUS_3              15                42
D57V10, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              46               117
  CLUS_2              32                83
  CLUS_3              43                77

Clustering(58) Variable = 9q loss mutation analysis
D58V1, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               1                 4
  CLUS_2               1                 8
  CLUS_3               4                 8
  CLUS_4               3                 3
D58V2, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               3                 4
  CLUS_2               4                 9
  CLUS_3               2                10
D58V3, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              44               104
  CLUS_2              22               166
  CLUS_3              37                50
  CLUS_4              14                35
D58V4, multiclass
D58V5, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              20                65
  CLUS_2              15                60
  CLUS_3              23                52
D58V6, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               2                21
  CLUS_2              22                67
  CLUS_3              21                44
  CLUS_4              13                45
D58V7, multiclass
D58V8, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              30               122
  CLUS_2              39                66
  CLUS_3              22                73
D58V9, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              34               124
  CLUS_2              54               129
  CLUS_3              11                46
D58V10, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              30               133
  CLUS_2              26                89
  CLUS_3              43                77

Clustering(59) Variable = 10p loss mutation analysis
D59V1, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                  4
  CLUS_2                1                  8
  CLUS_3                1                 11
  CLUS_4                1                  5
D59V2, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                1                 12
  CLUS_3                2                 10
D59V3, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               18                130
  CLUS_2                4                184
  CLUS_3               10                 77
  CLUS_4                3                 46
D59V4, multiclass
D59V5, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                7                 78
  CLUS_2                2                 73
  CLUS_3               10                 65
D59V6, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                 22
  CLUS_2               11                 78
  CLUS_3                6                 59
  CLUS_4                1                 57
D59V7, multiclass
D59V8, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               10                142
  CLUS_2               13                 92
  CLUS_3                3                 92
D59V9, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                6                152
  CLUS_2               20                163
  CLUS_3                7                 50
D59V10, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                9                154
  CLUS_2               14                101
  CLUS_3               10                110

Clustering(60) Variable = 10q loss mutation analysis
D60V1, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                1                  4
  CLUS_2                1                  8
  CLUS_3                1                 11
  CLUS_4                0                  6
D60V2, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                1                 12
  CLUS_3                2                 10
D60V3, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               25                123
  CLUS_2                8                180
  CLUS_3                7                 80
  CLUS_4                5                 44
D60V4, multiclass
D60V5, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                9                 76
  CLUS_2                2                 73
  CLUS_3               12                 63
D60V6, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                2                 21
  CLUS_2               12                 77
  CLUS_3                8                 57
  CLUS_4                1                 57
D60V7, multiclass
D60V8, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               13                139
  CLUS_2               14                 91
  CLUS_3                7                 88
D60V9, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               12                146
  CLUS_2               23                160
  CLUS_3                4                 53
D60V10, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               14                149
  CLUS_2               11                104
  CLUS_3               14                106

Clustering(61) Variable = 11p loss mutation analysis
D61V1, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                  4
  CLUS_2                1                  8
  CLUS_3                0                 12
  CLUS_4                1                  5
D61V2, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                2                  5
  CLUS_2                0                 13
  CLUS_3                1                 11
D61V3, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               13                135
  CLUS_2                3                185
  CLUS_3               11                 76
  CLUS_4                5                 44
D61V4, multiclass
D61V5, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                5                 80
  CLUS_2                2                 73
  CLUS_3               13                 62
D61V6, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                0                 23
  CLUS_2                7                 82
  CLUS_3               11                 54
  CLUS_4                2                 56
D61V7, multiclass
D61V8, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                3                149
  CLUS_2                9                 96
  CLUS_3               12                 83
D61V9, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                7                151
  CLUS_2               17                166
  CLUS_3                1                 56
D61V10, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                6                157
  CLUS_2               10                105
  CLUS_3                9                111

Clustering(62) Variable = 11q loss mutation analysis
D62V1, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                1                  4
  CLUS_2                0                  9
  CLUS_3                1                 11
  CLUS_4                1                  5
D62V2, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                  5
  CLUS_2                1                 12
  CLUS_3                0                 12
D62V3, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               13                135
  CLUS_2                3                185
  CLUS_3                8                 79
  CLUS_4                5                 44
D62V4, multiclass
D62V5, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                 83
  CLUS_2                2                 73
  CLUS_3               10                 65
D62V6, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                1                 22
  CLUS_2                2                 87
  CLUS_3                9                 56
  CLUS_4                2                 56
D62V7, multiclass
D62V8, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                6                146
  CLUS_2                6                 99
  CLUS_3               10                 85
D62V9, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               12                146
  CLUS_2               11                172
  CLUS_3                1                 56
D62V10, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               10                153
  CLUS_2                7                108
  CLUS_3                7                113

Clustering(63) Variable = 12p loss mutation analysis
D63V1, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                0                  5
  CLUS_2                2                  7
  CLUS_3                1                 11
  CLUS_4                1                  5
D63V2, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                1                 12
  CLUS_3                2                 10
D63V3, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               16                132
  CLUS_2               14                174
  CLUS_3                3                 84
  CLUS_4                4                 45
D63V4, multiclass
D63V5, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                8                 77
  CLUS_2                8                 67
  CLUS_3                6                 69
D63V6, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                1                 22
  CLUS_2               11                 78
  CLUS_3                4                 61
  CLUS_4                6                 52
D63V7, multiclass
D63V8, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               17                135
  CLUS_2                8                 97
  CLUS_3                7                 88
D63V9, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               15                143
  CLUS_2               15                168
  CLUS_3                3                 54
D63V10, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               17                146
  CLUS_2                9                106
  CLUS_3                7                113

Clustering(64) Variable = 12q loss mutation analysis
D64V1, multiclass
D64V2, multiclass
D64V3, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               13                135
  CLUS_2                6                182
  CLUS_3                2                 85
  CLUS_4                2                 47
D64V4, multiclass
D64V5, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                6                 79
  CLUS_2                4                 71
  CLUS_3                4                 71
D64V6, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                2                 21
  CLUS_2                8                 81
  CLUS_3                2                 63
  CLUS_4                2                 56
D64V7, multiclass
D64V8, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               10                142
  CLUS_2                5                100
  CLUS_3                5                 90
D64V9, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                9                149
  CLUS_2                9                174
  CLUS_3                2                 55
D64V10, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               11                152
  CLUS_2                5                110
  CLUS_3                4                116

Clustering(65) Variable = 13q loss mutation analysis
D65V1, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                3                  2
  CLUS_2                2                  7
  CLUS_3                1                 11
  CLUS_4                3                  3
D65V2, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                4                  3
  CLUS_2                1                 12
  CLUS_3                4                  8
D65V3, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               58                 90
  CLUS_2                4                184
  CLUS_3               31                 56
  CLUS_4               16                 33
D65V4, multiclass
D65V5, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               23                 62
  CLUS_2               13                 62
  CLUS_3               20                 55
D65V6, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                2                 21
  CLUS_2               27                 62
  CLUS_3               20                 45
  CLUS_4                7                 51
D65V7, multiclass
D65V8, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               21                131
  CLUS_2               32                 73
  CLUS_3               30                 65
D65V9, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               25                133
  CLUS_2               56                127
  CLUS_3               11                 46
D65V10, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               27                136
  CLUS_2               33                 82
  CLUS_3               32                 88

Clustering(66) Variable = 14q loss mutation analysis
D66V1, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                1                  4
  CLUS_2                0                  9
  CLUS_3                2                 10
  CLUS_4                0                  6
D66V2, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                2                 11
  CLUS_3                0                 12
D66V3, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               18                130
  CLUS_2               11                177
  CLUS_3               13                 74
  CLUS_4                4                 45
D66V4, multiclass
D66V5, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                8                 77
  CLUS_2                3                 72
  CLUS_3               13                 62
D66V6, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                4                 19
  CLUS_2                4                 85
  CLUS_3               13                 52
  CLUS_4                3                 55
D66V7, multiclass
D66V8, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               15                137
  CLUS_2               12                 93
  CLUS_3               12                 83
D66V9, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               15                143
  CLUS_2               24                159
  CLUS_3                3                 54
D66V10, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               14                149
  CLUS_2               14                101
  CLUS_3               14                106

Clustering(67) Variable = 15q loss mutation analysis
D67V1, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                2                  3
  CLUS_2                2                  7
  CLUS_3                2                 10
  CLUS_4                0                  6
D67V2, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                2                 11
  CLUS_3                4                  8
D67V3, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               48                100
  CLUS_2                9                179
  CLUS_3               22                 65
  CLUS_4               16                 33
D67V4, multiclass
D67V5, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               18                 67
  CLUS_2               13                 62
  CLUS_3               19                 56
D67V6, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                2                 21
  CLUS_2               25                 64
  CLUS_3               17                 48
  CLUS_4                6                 52
D67V7, multiclass
D67V8, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               17                135
  CLUS_2               26                 79
  CLUS_3               33                 62
D67V9, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               20                138
  CLUS_2               52                131
  CLUS_3                8                 49
D67V10, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               17                146
  CLUS_2               27                 88
  CLUS_3               36                 84

Clustering(68) Variable = 16p loss mutation analysis
D68V1, multiclass
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1678         TCGA-64-1680 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-67-3774 
"16P LOSS WILD-TYPE" 
D68V2, multiclass
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1678         TCGA-64-1680 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-67-3774 
"16P LOSS WILD-TYPE" 
D68V3, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               15                133
  CLUS_2                4                184
  CLUS_3               13                 74
  CLUS_4                5                 44
D68V4, multiclass
D68V5, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                8                 77
  CLUS_2                2                 73
  CLUS_3               10                 65
D68V6, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                1                 22
  CLUS_2                9                 80
  CLUS_3                8                 57
  CLUS_4                2                 56
D68V7, multiclass
D68V8, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                8                144
  CLUS_2               14                 91
  CLUS_3                7                 88
D68V9, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               10                148
  CLUS_2               21                162
  CLUS_3                1                 56
D68V10, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                7                156
  CLUS_2               11                104
  CLUS_3               14                106

Clustering(69) Variable = 16q loss mutation analysis
D69V1, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                3                  2
  CLUS_2                0                  9
  CLUS_3                2                 10
  CLUS_4                0                  6
D69V2, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                2                 11
  CLUS_3                2                 10
D69V3, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               28                120
  CLUS_2                6                182
  CLUS_3               15                 72
  CLUS_4                7                 42
D69V4, multiclass
D69V5, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                9                 76
  CLUS_2                6                 69
  CLUS_3               19                 56
D69V6, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                5                 18
  CLUS_2               10                 79
  CLUS_3               16                 49
  CLUS_4                3                 55
D69V7, multiclass
D69V8, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               15                137
  CLUS_2               19                 86
  CLUS_3               14                 81
D69V9, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               17                141
  CLUS_2               32                151
  CLUS_3                2                 55
D69V10, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               15                148
  CLUS_2               15                100
  CLUS_3               21                 99

Clustering(70) Variable = 17p loss mutation analysis
D70V1, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                  1
  CLUS_2                2                  7
  CLUS_3                3                  9
  CLUS_4                3                  3
D70V2, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                  3
  CLUS_2                3                 10
  CLUS_3                5                  7
D70V3, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               53                 95
  CLUS_2               23                165
  CLUS_3               20                 67
  CLUS_4               13                 36
D70V4, multiclass
D70V5, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               29                 56
  CLUS_2               13                 62
  CLUS_3               19                 56
D70V6, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                5                 18
  CLUS_2               30                 59
  CLUS_3               15                 50
  CLUS_4               11                 47
D70V7, multiclass
D70V8, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               36                116
  CLUS_2               26                 79
  CLUS_3               27                 68
D70V9, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               36                122
  CLUS_2               46                137
  CLUS_3               15                 42
D70V10, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               35                128
  CLUS_2               32                 83
  CLUS_3               30                 90

Clustering(71) Variable = 17q loss mutation analysis
D71V1, multiclass
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-44-2666         TCGA-44-2668         TCGA-44-3398 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-44-3918         TCGA-44-3919         TCGA-44-4112 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-55-1592         TCGA-55-1594         TCGA-55-1595 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-67-3774 
"17Q LOSS WILD-TYPE" 
D71V2, multiclass
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-44-2666         TCGA-44-2668         TCGA-44-3398 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-44-3918         TCGA-44-3919         TCGA-44-4112 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-55-1592         TCGA-55-1594         TCGA-55-1595 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-67-3774 
"17Q LOSS WILD-TYPE" 
D71V3, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                9                139
  CLUS_2                3                185
  CLUS_3                3                 84
  CLUS_4                2                 47
D71V4, multiclass
D71V5, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                8                 77
  CLUS_2                1                 74
  CLUS_3                3                 72
D71V6, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                 22
  CLUS_2                6                 83
  CLUS_3                3                 62
  CLUS_4                2                 56
D71V7, multiclass
D71V8, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                8                144
  CLUS_2                2                103
  CLUS_3                4                 91
D71V9, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                5                153
  CLUS_2                7                176
  CLUS_3                3                 54
D71V10, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                6                157
  CLUS_2                6                109
  CLUS_3                3                117

Clustering(72) Variable = 18p loss mutation analysis
D72V1, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                  5
  CLUS_2                1                  8
  CLUS_3                1                 11
  CLUS_4                2                  4
D72V2, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                2                  5
  CLUS_2                1                 12
  CLUS_3                1                 11
D72V3, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               35                113
  CLUS_2               14                174
  CLUS_3               22                 65
  CLUS_4                4                 45
D72V4, multiclass
D72V5, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               15                 70
  CLUS_2               11                 64
  CLUS_3               12                 63
D72V6, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                5                 18
  CLUS_2               18                 71
  CLUS_3               10                 55
  CLUS_4                5                 53
D72V7, multiclass
D72V8, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               23                129
  CLUS_2               16                 89
  CLUS_3               18                 77
D72V9, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               23                135
  CLUS_2               28                155
  CLUS_3                7                 50
D72V10, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               25                138
  CLUS_2               19                 96
  CLUS_3               14                106

Clustering(73) Variable = 18q loss mutation analysis
D73V1, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                  5
  CLUS_2                1                  8
  CLUS_3                1                 11
  CLUS_4                2                  4
D73V2, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                2                  5
  CLUS_2                1                 12
  CLUS_3                1                 11
D73V3, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               52                 96
  CLUS_2               22                166
  CLUS_3               31                 56
  CLUS_4                3                 46
D73V4, multiclass
D73V5, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               25                 60
  CLUS_2               14                 61
  CLUS_3               18                 57
D73V6, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                8                 15
  CLUS_2               24                 65
  CLUS_3               17                 48
  CLUS_4                8                 50
D73V7, multiclass
D73V8, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               32                120
  CLUS_2               24                 81
  CLUS_3               30                 65
D73V9, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               32                126
  CLUS_2               44                139
  CLUS_3               11                 46
D73V10, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               35                128
  CLUS_2               25                 90
  CLUS_3               27                 93

Clustering(74) Variable = 19p loss mutation analysis
D74V1, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                1                  4
  CLUS_2                2                  7
  CLUS_3                3                  9
  CLUS_4                3                  3
D74V2, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                3                  4
  CLUS_2                3                 10
  CLUS_3                3                  9
D74V3, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               32                116
  CLUS_2               22                166
  CLUS_3               41                 46
  CLUS_4               17                 32
D74V4, multiclass
D74V5, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               22                 63
  CLUS_2               22                 53
  CLUS_3               19                 56
D74V6, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                4                 19
  CLUS_2               24                 65
  CLUS_3               17                 48
  CLUS_4               18                 40
D74V7, multiclass
D74V8, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               32                120
  CLUS_2               39                 66
  CLUS_3               25                 70
D74V9, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               38                120
  CLUS_2               54                129
  CLUS_3                3                 54
D74V10, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               35                128
  CLUS_2               22                 93
  CLUS_3               38                 82

Clustering(75) Variable = 19q loss mutation analysis
D75V1, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                0                  5
  CLUS_2                2                  7
  CLUS_3                2                 10
  CLUS_4                2                  4
D75V2, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                2                  5
  CLUS_2                2                 11
  CLUS_3                2                 10
D75V3, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               27                121
  CLUS_2               12                176
  CLUS_3               21                 66
  CLUS_4                7                 42
D75V4, multiclass
D75V5, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               16                 69
  CLUS_2               12                 63
  CLUS_3               11                 64
D75V6, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                2                 21
  CLUS_2               18                 71
  CLUS_3                8                 57
  CLUS_4               11                 47
D75V7, multiclass
D75V8, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               17                135
  CLUS_2               21                 84
  CLUS_3               18                 77
D75V9, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               18                140
  CLUS_2               34                149
  CLUS_3                3                 54
D75V10, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               16                147
  CLUS_2               16                 99
  CLUS_3               23                 97

Clustering(76) Variable = 20p loss mutation analysis
D76V1, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                1                  4
  CLUS_2                0                  9
  CLUS_3                1                 11
  CLUS_4                2                  4
D76V2, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                  5
  CLUS_2                1                 12
  CLUS_3                1                 11
D76V3, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1               30                118
  CLUS_2               11                177
  CLUS_3               16                 71
  CLUS_4                4                 45
D76V4, multiclass
D76V5, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1               19                 66
  CLUS_2                4                 71
  CLUS_3               12                 63
D76V6, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                4                 19
  CLUS_2               20                 69
  CLUS_3                8                 57
  CLUS_4                3                 55
D76V7, multiclass
D76V8, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1               14                138
  CLUS_2               18                 87
  CLUS_3               18                 77
D76V9, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1               17                141
  CLUS_2               26                157
  CLUS_3                7                 50
D76V10, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1               19                144
  CLUS_2               12                103
  CLUS_3               19                101

Clustering(77) Variable = 20q loss mutation analysis
D77V1, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1680         TCGA-67-3770 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3774 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D77V2, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1680         TCGA-67-3770 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3774 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D77V3, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                5                143
  CLUS_2                8                180
  CLUS_3                7                 80
  CLUS_4                4                 45
D77V4, multiclass
D77V5, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                7                 78
  CLUS_2                2                 73
  CLUS_3                4                 71
D77V6, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                3                 20
  CLUS_2                3                 86
  CLUS_3                4                 61
  CLUS_4                3                 55
D77V7, multiclass
D77V8, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                9                143
  CLUS_2                6                 99
  CLUS_3                4                 91
D77V9, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                8                150
  CLUS_2               10                173
  CLUS_3                2                 55
D77V10, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1               11                152
  CLUS_2                2                113
  CLUS_3                7                113

Clustering(78) Variable = 21q loss mutation analysis
D78V1, multiclass
[1] "Remove cluster labels:" "21Q LOSS MUTATED"      
clus
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1595         TCGA-55-1596 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-64-1676         TCGA-64-1677         TCGA-64-1678 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-64-1680         TCGA-67-3770         TCGA-67-3771 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-67-3772         TCGA-67-3773         TCGA-67-3774 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
D78V2, multiclass
[1] "Remove cluster labels:" "21Q LOSS MUTATED"      
clus
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1595         TCGA-55-1596 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-64-1676         TCGA-64-1677         TCGA-64-1678 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-64-1680         TCGA-67-3770         TCGA-67-3771 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-67-3772         TCGA-67-3773         TCGA-67-3774 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
D78V3, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               13                135
  CLUS_2                8                180
  CLUS_3               30                 57
  CLUS_4               15                 34
D78V4, multiclass
D78V5, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                8                 77
  CLUS_2               10                 65
  CLUS_3               16                 59
D78V6, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                 21
  CLUS_2                6                 83
  CLUS_3               15                 50
  CLUS_4               11                 47
D78V7, multiclass
D78V8, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               11                141
  CLUS_2               33                 72
  CLUS_3                8                 87
D78V9, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               11                147
  CLUS_2               42                141
  CLUS_3                3                 54
D78V10, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               12                151
  CLUS_2               12                103
  CLUS_3               32                 88

Clustering(79) Variable = 22q loss mutation analysis
D79V1, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                2                  3
  CLUS_2                1                  8
  CLUS_3                1                 11
  CLUS_4                0                  6
D79V2, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                1                 12
  CLUS_3                3                  9
D79V3, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               39                109
  CLUS_2               10                178
  CLUS_3               24                 63
  CLUS_4               17                 32
D79V4, multiclass
D79V5, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               20                 65
  CLUS_2               10                 65
  CLUS_3               26                 49
D79V6, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                4                 19
  CLUS_2               19                 70
  CLUS_3               25                 40
  CLUS_4                8                 50
D79V7, multiclass
D79V8, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               19                133
  CLUS_2               34                 71
  CLUS_3               23                 72
D79V9, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               23                135
  CLUS_2               50                133
  CLUS_3                6                 51
D79V10, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               18                145
  CLUS_2               24                 91
  CLUS_3               37                 83

Clustering(80) Variable = Xq loss mutation analysis
D80V1, multiclass
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2                30 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1594 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-55-1596        TCGA-64-1676        TCGA-64-1677        TCGA-64-1678 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-64-1680        TCGA-67-3770        TCGA-67-3771        TCGA-67-3772 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-67-3773        TCGA-67-3774 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D80V2, multiclass
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2                30 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1594 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-55-1596        TCGA-64-1676        TCGA-64-1677        TCGA-64-1678 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-64-1680        TCGA-67-3770        TCGA-67-3771        TCGA-67-3772 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-67-3773        TCGA-67-3774 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D80V3, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               4               144
  CLUS_2               3               185
  CLUS_3               1                86
  CLUS_4               3                46
D80V4, multiclass
D80V5, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                84
  CLUS_2               2                73
  CLUS_3               2                73
D80V6, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                23
  CLUS_2               1                88
  CLUS_3               3                62
  CLUS_4               1                57
D80V7, multiclass
D80V8, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               3               149
  CLUS_2               5               100
  CLUS_3               1                94
D80V9, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               4               154
  CLUS_2               5               178
  CLUS_3               0                57
D80V10, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               3               160
  CLUS_2               2               113
  CLUS_3               4               116
                     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")
