
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/375851/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/SARC-TP/2907539/1.GDAC_mergedClustering.Finished/SARC-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SARC-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=SARC-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=52, in cluster file=51, common to both=51
[1] "Reduce the number of clustering variables from 80 to 65."
[1] 65 51
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                8                43 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                8                43 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                7                44 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                7                44 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5                46 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5                46 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               12                39 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               12                39 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                9                42 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                9                42 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7                44 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7                44 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                9                42 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                9                42 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               13                38 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               13                38 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               11                40 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               11                40 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                9                42 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                9                42 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                8                43 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                8                43 
[1] "9p gain mutation analysis"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3                48 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3                48 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                6                45 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                6                45 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 3                 48 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 3                 48 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 7                 44 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 7                 44 
[1] "14q gain mutation analysis"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                 48 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                 48 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 8                 43 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 8                 43 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 6                 45 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 6                 45 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 7                 44 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 7                 44 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 5                 46 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 5                 46 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                 45 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                 45 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 8                 43 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 8                 43 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 9                 42 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 9                 42 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 5                 46 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 5                 46 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                11                 40 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                11                 40 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                14                 37 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                14                 37 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 6                 45 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 6                 45 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                 46 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                 46 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                9                42 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                9                42 
[1] "1q loss mutation analysis"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                6                45 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                6                45 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10                41 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10                41 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                8                43 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                8                43 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               10                41 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               10                41 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               12                39 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               12                39 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                7                44 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                7                44 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                7                44 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                7                44 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                47 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                47 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                4                47 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                4                47 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                8                43 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                8                43 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                4                47 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                4                47 
[1] "7p loss mutation analysis"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                4                47 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                4                47 
[1] "7q loss mutation analysis"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6                45 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6                45 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                9                42 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                9                42 
[1] "8q loss mutation analysis"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                5                46 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                5                46 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               11                40 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               11                40 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                6                45 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                6                45 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                17                 34 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                17                 34 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                20                 31 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                20                 31 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                15                 36 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                15                 36 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                11                 40 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                11                 40 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                 47 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                 47 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                23                 28 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                23                 28 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                15                 36 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                15                 36 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 9                 42 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 9                 42 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                 42 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                 42 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                20                 31 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                20                 31 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 8                 43 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 8                 43 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 5                 46 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 5                 46 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 8                 43 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 8                 43 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                10                 41 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                10                 41 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 5                 46 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 5                 46 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 5                 46 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 5                 46 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                 43 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                 43 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                15                 36 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                15                 36 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               10                41 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               10                41 
[1] "data2feature, selection=ALL"
[1] "CN_CNMF"              "METHLYATION_CNMF"     "MIRSEQ_CNMF"         
[4] "MIRSEQ_CHIERARCHICAL"

Input Data has 4 rows and 51 columns.

Variable 1:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MIRSEQ_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"              "METHLYATION_CNMF"     "MIRSEQ_CNMF"         
[4] "MIRSEQ_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 51 columns, 0 survival variables, and 4 non-survival variables.
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=2, 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                13
  CLUS_2               2                14
  CLUS_3               6                16
D1V2, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               1                14
  CLUS_3               5                13
D1V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1    2
  1P GAIN WILD-TYPE   15   11
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1                15
  CLUS_2               2                11
D1V4, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               2                10
  CLUS_3               1                15

Clustering(2) Variable = 1q gain mutation analysis
D2V1, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               0                13
  CLUS_2               2                14
  CLUS_3               5                17
D2V2, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               1                17
  CLUS_2               0                15
  CLUS_3               6                12
D2V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      0    3
  1Q GAIN WILD-TYPE   16   10
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               0                16
  CLUS_2               3                10
D2V4, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               3                 9
  CLUS_3               0                16

Clustering(3) Variable = 4p gain mutation analysis
D3V1, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               2                11
  CLUS_2               2                14
  CLUS_3               1                21
D3V2, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               1                17
  CLUS_2               3                12
  CLUS_3               1                17
D3V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    0
  4P GAIN WILD-TYPE   16   13
D3V4, multiclass

Clustering(4) Variable = 5p gain mutation analysis
D4V1, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               1                12
  CLUS_2               7                 9
  CLUS_3               4                18
D4V2, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               4                14
  CLUS_2               4                11
  CLUS_3               4                14
D4V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2    2
  5P GAIN WILD-TYPE   14   11
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                14
  CLUS_2               2                11
D4V4, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               2                10
  CLUS_3               2                14

Clustering(5) Variable = 5q gain mutation analysis
D5V1, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1                12
  CLUS_2               6                10
  CLUS_3               2                20
D5V2, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               5                10
  CLUS_3               2                16
D5V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      2    1
  5Q GAIN WILD-TYPE   14   12
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                14
  CLUS_2               1                12
D5V4, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               1                11
  CLUS_3               2                14

Clustering(6) Variable = 6p gain mutation analysis
D6V1, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               3                10
  CLUS_2               4                12
  CLUS_3               0                22
D6V2, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               4                14
  CLUS_2               3                12
  CLUS_3               0                18
D6V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      4    0
  6P GAIN WILD-TYPE   12   13
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               4                12
  CLUS_2               0                13
D6V4, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               0                12
  CLUS_3               4                12

Clustering(7) Variable = 6q gain mutation analysis
D7V1, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               5                 8
  CLUS_2               3                13
  CLUS_3               1                21
D7V2, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               5                13
  CLUS_2               4                11
  CLUS_3               0                18
D7V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      5    0
  6Q GAIN WILD-TYPE   11   13
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               5                11
  CLUS_2               0                13
D7V4, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               0                12
  CLUS_3               5                11

Clustering(8) Variable = 7p gain mutation analysis
D8V1, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               1                12
  CLUS_2               9                 7
  CLUS_3               3                19
D8V2, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               6                12
  CLUS_2               5                10
  CLUS_3               2                16
D8V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      2    3
  7P GAIN WILD-TYPE   14   10
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               2                14
  CLUS_2               3                10
D8V4, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               1                 0
  CLUS_2               2                10
  CLUS_3               2                14

Clustering(9) Variable = 7q gain mutation analysis
D9V1, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               1                12
  CLUS_2               7                 9
  CLUS_3               3                19
D9V2, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               5                13
  CLUS_2               5                10
  CLUS_3               1                17
D9V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2    3
  7Q GAIN WILD-TYPE   14   10
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               2                14
  CLUS_2               3                10
D9V4, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               1                 0
  CLUS_2               2                10
  CLUS_3               2                14

Clustering(10) Variable = 8p gain mutation analysis
D10V1, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               0                13
  CLUS_2               6                10
  CLUS_3               3                19
D10V2, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               4                11
  CLUS_3               3                15
D10V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2    3
  8P GAIN WILD-TYPE   14   10
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               2                14
  CLUS_2               3                10
D10V4, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               3                 9
  CLUS_3               2                14

Clustering(11) Variable = 8q gain mutation analysis
D11V1, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1                12
  CLUS_2               4                12
  CLUS_3               3                19
D11V2, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               0                18
  CLUS_2               4                11
  CLUS_3               4                14
D11V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      2    2
  8Q GAIN WILD-TYPE   14   11
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2                14
  CLUS_2               2                11
D11V4, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               2                10
  CLUS_3               2                14

Clustering(12) Variable = 9p gain mutation analysis
D12V1, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2                11
  CLUS_2               1                15
  CLUS_3               0                22
D12V2, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               1                14
  CLUS_3               0                18
D12V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    0
  9P GAIN WILD-TYPE   14   13
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2                14
  CLUS_2               0                13
D12V4, multiclass
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                27 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DX-A3LS        TCGA-DX-A3LT        TCGA-DX-A3LW        TCGA-DX-A3M1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DX-A3M2        TCGA-DX-A3U5        TCGA-FX-A2QS        TCGA-FX-A3NJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FX-A3NK        TCGA-FX-A3RE        TCGA-HB-A2OT        TCGA-HB-A3L4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IE-A3OV        TCGA-IF-A3RQ        TCGA-IS-A3K6        TCGA-IS-A3K7 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IS-A3K8        TCGA-IS-A3KA        TCGA-IW-A3M4        TCGA-IW-A3M5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IW-A3M6        TCGA-K1-A3PN        TCGA-K1-A3PO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 

Clustering(13) Variable = 9q gain mutation analysis
D13V1, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               4                 9
  CLUS_2               2                14
  CLUS_3               0                22
D13V2, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               3                12
  CLUS_3               1                17
D13V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      4    0
  9Q GAIN WILD-TYPE   12   13
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               4                12
  CLUS_2               0                13
D13V4, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               0                12
  CLUS_3               4                12

Clustering(14) Variable = 11p gain mutation analysis
D14V1, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                2                 14
  CLUS_3                1                 21
D14V2, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                1                 14
  CLUS_3                1                 17
D14V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0    1
  11P GAIN WILD-TYPE   16   12
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                 16
  CLUS_2                1                 12
D14V4, multiclass
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 28 
        TCGA-DX-A2IZ         TCGA-DX-A2J0         TCGA-DX-A2J1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DX-A2J4         TCGA-DX-A3LS         TCGA-DX-A3LT 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DX-A3LU         TCGA-DX-A3LW         TCGA-DX-A3M1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DX-A3M2         TCGA-DX-A3U5         TCGA-FX-A2QS 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FX-A3NJ         TCGA-FX-A3NK         TCGA-FX-A3RE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FX-A3TO         TCGA-HB-A2OT         TCGA-HB-A3L4 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IE-A3OV         TCGA-IF-A3RQ         TCGA-IS-A3K6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IS-A3K7         TCGA-IS-A3K8         TCGA-IW-A3M4 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IW-A3M5         TCGA-IW-A3M6         TCGA-K1-A3PN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-K1-A3PO 
"11P GAIN WILD-TYPE" 

Clustering(15) Variable = 12p gain mutation analysis
D15V1, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                2                 14
  CLUS_3                3                 19
D15V2, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                3                 12
  CLUS_3                2                 16
D15V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1    0
  12P GAIN WILD-TYPE   15   13
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                0                 13
D15V4, multiclass
[1] "Remove cluster labels:" "12P GAIN MUTATED"      
clus
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 1                 28 
        TCGA-DX-A2IZ         TCGA-DX-A2J0         TCGA-DX-A2J1 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DX-A2J4         TCGA-DX-A3LT         TCGA-DX-A3LU 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DX-A3LW         TCGA-DX-A3M1         TCGA-DX-A3M2 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DX-A3U5         TCGA-FX-A2QS         TCGA-FX-A3NJ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FX-A3NK         TCGA-FX-A3RE         TCGA-FX-A3TO 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-HB-A2OT         TCGA-HB-A3L4         TCGA-IE-A3OV 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-IF-A3RQ         TCGA-IS-A3K6         TCGA-IS-A3K7 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-IS-A3K8         TCGA-IS-A3KA         TCGA-IW-A3M4 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-IW-A3M5         TCGA-IW-A3M6         TCGA-K1-A3PN 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-K1-A3PO 
"12P GAIN WILD-TYPE" 

Clustering(16) Variable = 14q gain mutation analysis
D16V1, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                1                 15
  CLUS_3                1                 21
D16V2, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                2                 13
  CLUS_3                1                 17
D16V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1    0
  14Q GAIN WILD-TYPE   15   13
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                0                 13
D16V4, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                 28 
        TCGA-DX-A2IZ         TCGA-DX-A2J0         TCGA-DX-A2J1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DX-A2J4         TCGA-DX-A3LS         TCGA-DX-A3LT 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DX-A3LU         TCGA-DX-A3LW         TCGA-DX-A3M1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DX-A3M2         TCGA-DX-A3U5         TCGA-FX-A2QS 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FX-A3NJ         TCGA-FX-A3NK         TCGA-FX-A3RE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FX-A3TO         TCGA-HB-A2OT         TCGA-HB-A3L4 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IE-A3OV         TCGA-IF-A3RQ         TCGA-IS-A3K6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IS-A3K7         TCGA-IS-A3K8         TCGA-IS-A3KA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IW-A3M4         TCGA-IW-A3M6         TCGA-K1-A3PN 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-K1-A3PO 
"14Q GAIN WILD-TYPE" 

Clustering(17) Variable = 15q gain mutation analysis
D17V1, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                3                 13
  CLUS_3                5                 17
D17V2, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                2                 13
  CLUS_3                4                 14
D17V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1    1
  15Q GAIN WILD-TYPE   15   12
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                1                 12
D17V4, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                 27 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DX-A3LS         TCGA-DX-A3LT         TCGA-DX-A3LU 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DX-A3LW         TCGA-DX-A3M1         TCGA-DX-A3M2 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DX-A3U5         TCGA-FX-A2QS         TCGA-FX-A3NJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FX-A3NK         TCGA-FX-A3RE         TCGA-FX-A3TO 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HB-A2OT         TCGA-HB-A3L4         TCGA-IE-A3OV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IF-A3RQ         TCGA-IS-A3K6         TCGA-IS-A3K7 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IS-A3K8         TCGA-IW-A3M4         TCGA-IW-A3M5 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IW-A3M6         TCGA-K1-A3PN         TCGA-K1-A3PO 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 

Clustering(18) Variable = 16p gain mutation analysis
D18V1, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                1                 15
  CLUS_3                4                 18
D18V2, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                3                 12
  CLUS_3                3                 15
D18V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1    2
  16P GAIN WILD-TYPE   15   11
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                2                 11
D18V4, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                2                 10
  CLUS_3                1                 15

Clustering(19) Variable = 17p gain mutation analysis
D19V1, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                6                 10
  CLUS_3                0                 22
D19V2, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                6                  9
  CLUS_3                0                 18
D19V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1    1
  17P GAIN WILD-TYPE   15   12
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                1                 12
D19V4, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                 27 
        TCGA-DX-A2IZ         TCGA-DX-A2J0         TCGA-DX-A2J1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DX-A2J4         TCGA-DX-A3LS         TCGA-DX-A3LT 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DX-A3LU         TCGA-DX-A3LW         TCGA-DX-A3M1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DX-A3M2         TCGA-DX-A3U5         TCGA-FX-A2QS 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FX-A3NJ         TCGA-FX-A3NK         TCGA-HB-A2OT 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HB-A3L4         TCGA-IE-A3OV         TCGA-IF-A3RQ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-IS-A3K6         TCGA-IS-A3K7         TCGA-IS-A3K8 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-IS-A3KA         TCGA-IW-A3M4         TCGA-IW-A3M5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-IW-A3M6         TCGA-K1-A3PN         TCGA-K1-A3PO 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 

Clustering(20) Variable = 17q gain mutation analysis
D20V1, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                4                 12
  CLUS_3                1                 21
D20V2, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                3                 12
  CLUS_3                1                 17
D20V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1    2
  17Q GAIN WILD-TYPE   15   11
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                2                 11
D20V4, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                  0
  CLUS_2                1                 11
  CLUS_3                1                 15

Clustering(21) Variable = 18p gain mutation analysis
D21V1, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                3                 13
  CLUS_3                3                 19
D21V2, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                3                 12
  CLUS_3                2                 16
D21V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1    1
  18P GAIN WILD-TYPE   15   12
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                1                 12
D21V4, multiclass
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                 27 
        TCGA-DX-A2IZ         TCGA-DX-A2J0         TCGA-DX-A2J1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DX-A2J4         TCGA-DX-A3LS         TCGA-DX-A3LT 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DX-A3LU         TCGA-DX-A3LW         TCGA-DX-A3M1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DX-A3M2         TCGA-DX-A3U5         TCGA-FX-A2QS 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FX-A3NJ         TCGA-FX-A3NK         TCGA-FX-A3RE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-HB-A2OT         TCGA-HB-A3L4         TCGA-IE-A3OV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IF-A3RQ         TCGA-IS-A3K6         TCGA-IS-A3K7 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IS-A3K8         TCGA-IW-A3M4         TCGA-IW-A3M5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IW-A3M6         TCGA-K1-A3PN         TCGA-K1-A3PO 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 

Clustering(22) Variable = 18q gain mutation analysis
D22V1, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                4                 12
  CLUS_3                3                 19
D22V2, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                4                 11
  CLUS_3                2                 16
D22V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2    1
  18Q GAIN WILD-TYPE   14   12
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                1                 12
D22V4, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                1                 11
  CLUS_3                2                 14

Clustering(23) Variable = 19p gain mutation analysis
D23V1, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                7                  9
  CLUS_3                2                 20
D23V2, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                4                 11
  CLUS_3                3                 15
D23V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1    2
  19P GAIN WILD-TYPE   15   11
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                2                 11
D23V4, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                  0
  CLUS_2                1                 11
  CLUS_3                1                 15

Clustering(24) Variable = 19q gain mutation analysis
D24V1, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                5                 11
  CLUS_3                0                 22
D24V2, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                2                 13
  CLUS_3                1                 17
D24V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0    0
  19Q GAIN WILD-TYPE   16   13
D24V4, multiclass

Clustering(25) Variable = 20p gain mutation analysis
D25V1, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                5                 11
  CLUS_3                5                 17
D25V2, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                5                 10
  CLUS_3                4                 14
D25V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2    2
  20P GAIN WILD-TYPE   14   11
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                2                 11
D25V4, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                2                 10
  CLUS_3                2                 14

Clustering(26) Variable = 20q gain mutation analysis
D26V1, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                3                 10
  CLUS_2                7                  9
  CLUS_3                4                 18
D26V2, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                8                  7
  CLUS_3                3                 15
D26V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3    2
  20Q GAIN WILD-TYPE   13   11
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                2                 11
D26V4, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                2                 10
  CLUS_3                3                 13

Clustering(27) Variable = 21q gain mutation analysis
D27V1, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                3                 13
  CLUS_3                2                 20
D27V2, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                4                 11
  CLUS_3                1                 17
D27V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1    1
  21Q GAIN WILD-TYPE   15   12
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                1                 12
D27V4, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 27 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DX-A3LS         TCGA-DX-A3LT         TCGA-DX-A3LU 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DX-A3LW         TCGA-DX-A3M1         TCGA-DX-A3M2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DX-A3U5         TCGA-FX-A2QS         TCGA-FX-A3NJ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FX-A3NK         TCGA-FX-A3RE         TCGA-FX-A3TO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-HB-A2OT         TCGA-HB-A3L4         TCGA-IF-A3RQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-IS-A3K6         TCGA-IS-A3K7         TCGA-IS-A3K8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-IS-A3KA         TCGA-IW-A3M4         TCGA-IW-A3M5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-IW-A3M6         TCGA-K1-A3PN         TCGA-K1-A3PO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 

Clustering(28) Variable = 22q gain mutation analysis
D28V1, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                2                 14
  CLUS_3                2                 20
D28V2, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                1                 14
  CLUS_3                2                 16
D28V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0    1
  22Q GAIN WILD-TYPE   16   12
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                0                 16
  CLUS_2                1                 12
D28V4, multiclass
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 28 
        TCGA-DX-A2IZ         TCGA-DX-A2J0         TCGA-DX-A2J1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DX-A2J4         TCGA-DX-A3LS         TCGA-DX-A3LT 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DX-A3LU         TCGA-DX-A3LW         TCGA-DX-A3M1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DX-A3M2         TCGA-DX-A3U5         TCGA-FX-A2QS 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FX-A3NJ         TCGA-FX-A3NK         TCGA-FX-A3RE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FX-A3TO         TCGA-HB-A3L4         TCGA-IE-A3OV 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IF-A3RQ         TCGA-IS-A3K6         TCGA-IS-A3K7 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IS-A3K8         TCGA-IS-A3KA         TCGA-IW-A3M4 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IW-A3M5         TCGA-IW-A3M6         TCGA-K1-A3PN 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-K1-A3PO 
"22Q GAIN WILD-TYPE" 

Clustering(29) Variable = 1p loss mutation analysis
D29V1, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               6                10
  CLUS_3               2                20
D29V2, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               3                12
  CLUS_3               5                13
D29V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    4
  1P LOSS WILD-TYPE   15    9
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                15
  CLUS_2               4                 9
D29V4, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                 0
  CLUS_2               3                 9
  CLUS_3               1                15

Clustering(30) Variable = 1q loss mutation analysis
D30V1, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               2                11
  CLUS_2               3                13
  CLUS_3               1                21
D30V2, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               2                16
  CLUS_2               2                13
  CLUS_3               2                16
D30V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2    1
  1Q LOSS WILD-TYPE   14   12
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               2                14
  CLUS_2               1                12
D30V4, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               1                11
  CLUS_3               2                14

Clustering(31) Variable = 2p loss mutation analysis
D31V1, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               2                11
  CLUS_2               3                13
  CLUS_3               5                17
D31V2, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               4                11
  CLUS_3               5                13
D31V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2    3
  2P LOSS WILD-TYPE   14   10
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               2                14
  CLUS_2               3                10
D31V4, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               3                 9
  CLUS_3               2                14

Clustering(32) Variable = 2q loss mutation analysis
D32V1, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               2                11
  CLUS_2               3                13
  CLUS_3               3                19
D32V2, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               4                11
  CLUS_3               3                15
D32V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2    2
  2Q LOSS WILD-TYPE   14   11
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               2                14
  CLUS_2               2                11
D32V4, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               2                10
  CLUS_3               2                14

Clustering(33) Variable = 3p loss mutation analysis
D33V1, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               5                 8
  CLUS_2               3                13
  CLUS_3               2                20
D33V2, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               4                14
  CLUS_2               4                11
  CLUS_3               2                16
D33V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      4    0
  3P LOSS WILD-TYPE   12   13
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               4                12
  CLUS_2               0                13
D33V4, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               0                12
  CLUS_3               4                12

Clustering(34) Variable = 3q loss mutation analysis
D34V1, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               5                 8
  CLUS_2               3                13
  CLUS_3               4                18
D34V2, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               4                14
  CLUS_2               5                10
  CLUS_3               3                15
D34V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5    1
  3Q LOSS WILD-TYPE   11   12
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               5                11
  CLUS_2               1                12
D34V4, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               1                11
  CLUS_3               5                11

Clustering(35) Variable = 4p loss mutation analysis
D35V1, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               0                13
  CLUS_2               4                12
  CLUS_3               3                19
D35V2, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               0                18
  CLUS_2               3                12
  CLUS_3               4                14
D35V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      2    1
  4P LOSS WILD-TYPE   14   12
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               2                14
  CLUS_2               1                12
D35V4, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               1                11
  CLUS_3               2                14

Clustering(36) Variable = 4q loss mutation analysis
D36V1, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               0                13
  CLUS_2               3                13
  CLUS_3               4                18
D36V2, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               0                18
  CLUS_2               3                12
  CLUS_3               4                14
D36V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2    1
  4Q LOSS WILD-TYPE   14   12
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               2                14
  CLUS_2               1                12
D36V4, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               1                11
  CLUS_3               2                14

Clustering(37) Variable = 5p loss mutation analysis
D37V1, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               0                13
  CLUS_2               2                14
  CLUS_3               2                20
D37V2, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               2                16
  CLUS_2               0                15
  CLUS_3               2                16
D37V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2    1
  5P LOSS WILD-TYPE   14   12
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               2                14
  CLUS_2               1                12
D37V4, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               1                11
  CLUS_3               2                14

Clustering(38) Variable = 5q loss mutation analysis
D38V1, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               1                15
  CLUS_3               2                20
D38V2, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               1                14
  CLUS_3               2                16
D38V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      2    0
  5Q LOSS WILD-TYPE   14   13
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               2                14
  CLUS_2               0                13
D38V4, multiclass
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
clus
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                2                27 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DX-A3LS        TCGA-DX-A3LU        TCGA-DX-A3LW        TCGA-DX-A3M1 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DX-A3M2        TCGA-DX-A3U5        TCGA-FX-A3NJ        TCGA-FX-A3NK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FX-A3RE        TCGA-FX-A3TO        TCGA-HB-A2OT        TCGA-HB-A3L4 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-IE-A3OV        TCGA-IF-A3RQ        TCGA-IS-A3K6        TCGA-IS-A3K7 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-IS-A3K8        TCGA-IS-A3KA        TCGA-IW-A3M4        TCGA-IW-A3M5 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-IW-A3M6        TCGA-K1-A3PN        TCGA-K1-A3PO 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 

Clustering(39) Variable = 6p loss mutation analysis
D39V1, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               2                14
  CLUS_3               5                17
D39V2, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2                16
  CLUS_2               1                14
  CLUS_3               5                13
D39V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2    4
  6P LOSS WILD-TYPE   14    9
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2                14
  CLUS_2               4                 9
D39V4, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               4                 8
  CLUS_3               2                14

Clustering(40) Variable = 6q loss mutation analysis
D40V1, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               0                13
  CLUS_2               2                14
  CLUS_3               2                20
D40V2, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               0                18
  CLUS_2               1                14
  CLUS_3               3                15
D40V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1    1
  6Q LOSS WILD-TYPE   15   12
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               1                15
  CLUS_2               1                12
D40V4, multiclass
[1] "Remove cluster labels:" "6Q LOSS MUTATED"       
clus
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                2                27 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DX-A3LS        TCGA-DX-A3LT        TCGA-DX-A3LU        TCGA-DX-A3LW 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DX-A3M1        TCGA-DX-A3M2        TCGA-DX-A3U5        TCGA-FX-A2QS 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FX-A3NJ        TCGA-FX-A3NK        TCGA-FX-A3RE        TCGA-HB-A2OT 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-HB-A3L4        TCGA-IF-A3RQ        TCGA-IS-A3K6        TCGA-IS-A3K7 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-IS-A3K8        TCGA-IS-A3KA        TCGA-IW-A3M4        TCGA-IW-A3M5 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-IW-A3M6        TCGA-K1-A3PN        TCGA-K1-A3PO 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 

Clustering(41) Variable = 7p loss mutation analysis
D41V1, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0                13
  CLUS_2               2                14
  CLUS_3               2                20
D41V2, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0                18
  CLUS_2               1                14
  CLUS_3               3                15
D41V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1    2
  7P LOSS WILD-TYPE   15   11
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               1                15
  CLUS_2               2                11
D41V4, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               2                10
  CLUS_3               1                15

Clustering(42) Variable = 7q loss mutation analysis
D42V1, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               3                13
  CLUS_3               2                20
D42V2, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               0                18
  CLUS_2               3                12
  CLUS_3               3                15
D42V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3    1
  7Q LOSS WILD-TYPE   13   12
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               3                13
  CLUS_2               1                12
D42V4, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               1                11
  CLUS_3               3                13

Clustering(43) Variable = 8p loss mutation analysis
D43V1, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               3                10
  CLUS_2               4                12
  CLUS_3               2                20
D43V2, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               5                13
  CLUS_2               2                13
  CLUS_3               2                16
D43V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4    2
  8P LOSS WILD-TYPE   12   11
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               4                12
  CLUS_2               2                11
D43V4, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               1                 0
  CLUS_2               1                11
  CLUS_3               4                12

Clustering(44) Variable = 8q loss mutation analysis
D44V1, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               2                11
  CLUS_2               1                15
  CLUS_3               2                20
D44V2, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               4                14
  CLUS_2               0                15
  CLUS_3               1                17
D44V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3    0
  8Q LOSS WILD-TYPE   13   13
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               3                13
  CLUS_2               0                13
D44V4, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               0                12
  CLUS_3               3                13

Clustering(45) Variable = 9p loss mutation analysis
D45V1, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               3                10
  CLUS_2               6                10
  CLUS_3               2                20
D45V2, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               6                 9
  CLUS_3               2                16
D45V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      5    1
  9P LOSS WILD-TYPE   11   12
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               5                11
  CLUS_2               1                12
D45V4, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                 0
  CLUS_2               0                12
  CLUS_3               5                11

Clustering(46) Variable = 9q loss mutation analysis
D46V1, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               3                13
  CLUS_3               2                20
D46V2, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               2                13
  CLUS_3               1                17
D46V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      3    1
  9Q LOSS WILD-TYPE   13   12
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               3                13
  CLUS_2               1                12
D46V4, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               1                11
  CLUS_3               3                13

Clustering(47) Variable = 10p loss mutation analysis
D47V1, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                8                  8
  CLUS_3                7                 15
D47V2, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                6                  9
  CLUS_3                8                 10
D47V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4    4
  10P LOSS WILD-TYPE   12    9
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                4                 12
  CLUS_2                4                  9
D47V4, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                  0
  CLUS_2                3                  9
  CLUS_3                4                 12

Clustering(48) Variable = 10q loss mutation analysis
D48V1, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                6                 10
  CLUS_3               12                 10
D48V2, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                6                  9
  CLUS_3               11                  7
D48V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3    7
  10Q LOSS WILD-TYPE   13    6
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                7                  6
D48V4, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                1                  0
  CLUS_2                6                  6
  CLUS_3                3                 13

Clustering(49) Variable = 11p loss mutation analysis
D49V1, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                6                  7
  CLUS_2                4                 12
  CLUS_3                5                 17
D49V2, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                7                  8
  CLUS_3                4                 14
D49V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      5    2
  11P LOSS WILD-TYPE   11   11
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                5                 11
  CLUS_2                2                 11
D49V4, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                  0
  CLUS_2                1                 11
  CLUS_3                5                 11

Clustering(50) Variable = 11q loss mutation analysis
D50V1, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                6                  7
  CLUS_2                2                 14
  CLUS_3                3                 19
D50V2, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                5                 10
  CLUS_3                2                 16
D50V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      5    1
  11Q LOSS WILD-TYPE   11   12
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                5                 11
  CLUS_2                1                 12
D50V4, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                1                 11
  CLUS_3                5                 11

Clustering(51) Variable = 12q loss mutation analysis
D51V1, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                1                 15
  CLUS_3                3                 19
D51V2, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                1                 14
  CLUS_3                1                 17
D51V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2    0
  12Q LOSS WILD-TYPE   14   13
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                0                 13
D51V4, multiclass
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 2                 27 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DX-A3LT         TCGA-DX-A3LU         TCGA-DX-A3LW 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DX-A3M1         TCGA-DX-A3M2         TCGA-DX-A3U5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3NK 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FX-A3RE         TCGA-FX-A3TO         TCGA-HB-A2OT 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-HB-A3L4         TCGA-IE-A3OV         TCGA-IF-A3RQ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IS-A3K6         TCGA-IS-A3K7         TCGA-IS-A3K8 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IS-A3KA         TCGA-IW-A3M4         TCGA-IW-A3M5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IW-A3M6         TCGA-K1-A3PN         TCGA-K1-A3PO 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 

Clustering(52) Variable = 13q loss mutation analysis
D52V1, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                6                  7
  CLUS_2               10                  6
  CLUS_3                7                 15
D52V2, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                6                 12
  CLUS_2                9                  6
  CLUS_3                8                 10
D52V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      6    6
  13Q LOSS WILD-TYPE   10    7
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                6                 10
  CLUS_2                6                  7
D52V4, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                1                  0
  CLUS_2                5                  7
  CLUS_3                6                 10

Clustering(53) Variable = 14q loss mutation analysis
D53V1, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                5                  8
  CLUS_2                7                  9
  CLUS_3                3                 19
D53V2, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                6                 12
  CLUS_2                2                 13
  CLUS_3                7                 11
D53V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      3    6
  14Q LOSS WILD-TYPE   13    7
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                6                  7
D53V4, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                6                  6
  CLUS_3                3                 13

Clustering(54) Variable = 15q loss mutation analysis
D54V1, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                3                 10
  CLUS_2                4                 12
  CLUS_3                2                 20
D54V2, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                4                 11
  CLUS_3                1                 17
D54V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      7    0
  15Q LOSS WILD-TYPE    9   13
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                7                  9
  CLUS_2                0                 13
D54V4, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                0                 12
  CLUS_3                7                  9

Clustering(55) Variable = 16p loss mutation analysis
D55V1, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                4                 12
  CLUS_3                3                 19
D55V2, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                3                 12
  CLUS_3                3                 15
D55V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4    1
  16P LOSS WILD-TYPE   12   12
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                4                 12
  CLUS_2                1                 12
D55V4, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                1                 11
  CLUS_3                4                 12

Clustering(56) Variable = 16q loss mutation analysis
D56V1, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                5                  8
  CLUS_2                7                  9
  CLUS_3                8                 14
D56V2, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                7                  8
  CLUS_3               10                  8
D56V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      4    5
  16Q LOSS WILD-TYPE   12    8
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                4                 12
  CLUS_2                5                  8
D56V4, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                1                  0
  CLUS_2                4                  8
  CLUS_3                4                 12

Clustering(57) Variable = 17p loss mutation analysis
D57V1, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                1                 15
  CLUS_3                6                 16
D57V2, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                1                 14
  CLUS_3                5                 13
D57V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3    3
  17P LOSS WILD-TYPE   13   10
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                3                 10
D57V4, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                3                  9
  CLUS_3                3                 13

Clustering(58) Variable = 17q loss mutation analysis
D58V1, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                0                 16
  CLUS_3                5                 17
D58V2, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                0                 15
  CLUS_3                4                 14
D58V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    2
  17Q LOSS WILD-TYPE   15   11
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                2                 11
D58V4, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                2                 10
  CLUS_3                1                 15

Clustering(59) Variable = 18p loss mutation analysis
D59V1, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                2                 14
  CLUS_3                4                 18
D59V2, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                3                 12
  CLUS_3                2                 16
D59V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3    1
  18P LOSS WILD-TYPE   13   12
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                1                 12
D59V4, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                1                 11
  CLUS_3                3                 13

Clustering(60) Variable = 18q loss mutation analysis
D60V1, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                4                 12
  CLUS_3                4                 18
D60V2, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                3                 12
  CLUS_3                3                 15
D60V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3    1
  18Q LOSS WILD-TYPE   13   12
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                1                 12
D60V4, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                1                 11
  CLUS_3                3                 13

Clustering(61) Variable = 19q loss mutation analysis
D61V1, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                1                 15
  CLUS_3                2                 20
D61V2, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                2                 13
  CLUS_3                3                 15
D61V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    1
  19Q LOSS WILD-TYPE   15   12
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                1                 12
D61V4, multiclass
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                 27 
        TCGA-DX-A2IZ         TCGA-DX-A2J1         TCGA-DX-A2J4 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DX-A3LS         TCGA-DX-A3LT         TCGA-DX-A3LU 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DX-A3LW         TCGA-DX-A3M1         TCGA-DX-A3M2 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DX-A3U5         TCGA-FX-A2QS         TCGA-FX-A3NJ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FX-A3NK         TCGA-FX-A3RE         TCGA-FX-A3TO 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-HB-A2OT         TCGA-HB-A3L4         TCGA-IE-A3OV 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IF-A3RQ         TCGA-IS-A3K6         TCGA-IS-A3K7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IS-A3K8         TCGA-IS-A3KA         TCGA-IW-A3M5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IW-A3M6         TCGA-K1-A3PN         TCGA-K1-A3PO 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 

Clustering(62) Variable = 20p loss mutation analysis
D62V1, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                3                 10
  CLUS_2                0                 16
  CLUS_3                2                 20
D62V2, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                2                 13
  CLUS_3                1                 17
D62V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      4    1
  20P LOSS WILD-TYPE   12   12
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                4                 12
  CLUS_2                1                 12
D62V4, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                1                 11
  CLUS_3                4                 12

Clustering(63) Variable = 21q loss mutation analysis
D63V1, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                3                 10
  CLUS_2                4                 12
  CLUS_3                1                 21
D63V2, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                3                 12
  CLUS_3                2                 16
D63V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3    2
  21Q LOSS WILD-TYPE   13   11
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                2                 11
D63V4, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                2                 10
  CLUS_3                3                 13

Clustering(64) Variable = 22q loss mutation analysis
D64V1, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                6                 10
  CLUS_3                7                 15
D64V2, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                4                 11
  CLUS_3                7                 11
D64V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      7    4
  22Q LOSS WILD-TYPE    9    9
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                7                  9
  CLUS_2                4                  9
D64V4, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                0                  1
  CLUS_2                4                  8
  CLUS_3                7                  9

Clustering(65) Variable = Xq loss mutation analysis
D65V1, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               3                10
  CLUS_2               6                10
  CLUS_3               1                21
D65V2, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               6                 9
  CLUS_3               3                15
D65V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3    3
  XQ LOSS WILD-TYPE   13   10
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               3                13
  CLUS_2               3                10
D65V4, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                 1
  CLUS_2               3                 9
  CLUS_3               3                13
                    V1                     V2                     V3 
             "CN_CNMF"     "METHLYATION_CNMF"          "MIRSEQ_CNMF" 
                    V4 
"MIRSEQ_CHIERARCHICAL" 
> q(save="no")
