
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/399196/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/SKCM-All_Primary/3157297/1.GDAC_mergedClustering.Finished/SKCM-All_Primary.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SKCM-All_Primary", "-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=SKCM-All_Primary"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=58, in cluster file=46, common to both=46
[1] "Reduce the number of clustering variables from 80 to 47."
[1] 47 46
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                5                41 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                5                41 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               12                34 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               12                34 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                43 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                43 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                43 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                43 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3                43 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3                43 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                7                39 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                7                39 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                3                43 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                3                43 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               14                32 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               14                32 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                3                43 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                3                43 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               19                27 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               19                27 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               18                28 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               18                28 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                7                39 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                7                39 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               15                31 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               15                31 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 4                 42 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 4                 42 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 7                 39 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 7                 39 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 8                 38 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 8                 38 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 9                 37 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 9                 37 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                11                 35 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                11                 35 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                 43 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                 43 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                 41 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                 41 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                5                41 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                5                41 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                4                42 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                4                42 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                7                39 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                7                39 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                9                37 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                9                37 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6                40 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6                40 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               15                31 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               15                31 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               11                35 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               11                35 
[1] "8q loss mutation analysis"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                5                41 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                5                41 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               25                21 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               25                21 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               15                31 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               15                31 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                19                 27 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                19                 27 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                22                 24 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                22                 24 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 8                 38 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 8                 38 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                10                 36 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                10                 36 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 6                 40 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 6                 40 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 8                 38 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 8                 38 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 7                 39 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 7                 39 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 6                 40 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 6                 40 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                 43 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                 43 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                13                 33 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                13                 33 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 8                 38 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 8                 38 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 5                 41 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 5                 41 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                 41 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                 41 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                 42 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                 42 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 43 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 43 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 6                 40 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 6                 40 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 5                 41 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 5                 41 
[1] "data2feature, selection=ALL"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "RPPA_CNMF"            
[4] "RPPA_CHIERARCHICAL"    "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL"
[7] "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 8 rows and 46 columns.

Variable 1:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "RPPA_CNMF"            
[4] "RPPA_CHIERARCHICAL"    "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL"
[7] "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 46 columns, 0 survival variables, and 8 non-survival variables.
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=5, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=2, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, 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               1                13
  CLUS_2               2                11
  CLUS_3               2                17
D1V2, multiclass
D1V3, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               3                 6
  CLUS_2               0                 5
  CLUS_3               1                 6
D1V4, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               0                 5
  CLUS_3               3                 6
D1V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      4    1
  1P GAIN WILD-TYPE   23   15
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               4                23
  CLUS_2               1                15
D1V6, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               0                 3
  CLUS_3               4                22
D1V7, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      3    2
  1P GAIN WILD-TYPE   18   22
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               3                18
  CLUS_2               2                22
D1V8, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               1                 8
  CLUS_3               2                16

Clustering(2) Variable = 1q gain mutation analysis
D2V1, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               6                 7
  CLUS_3               5                14
D2V2, multiclass
D2V3, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               3                 6
  CLUS_2               2                 3
  CLUS_3               2                 5
D2V4, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                 5
  CLUS_2               2                 3
  CLUS_3               3                 6
D2V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      8    3
  1Q GAIN WILD-TYPE   19   13
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               8                19
  CLUS_2               3                13
D2V6, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                12
  CLUS_2               1                 2
  CLUS_3               8                18
D2V7, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      6    6
  1Q GAIN WILD-TYPE   15   18
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               6                15
  CLUS_2               6                18
D2V8, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               6                12
  CLUS_2               2                 7
  CLUS_3               4                14

Clustering(3) Variable = 3p gain mutation analysis
D3V1, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               1                12
  CLUS_3               1                18
D3V2, multiclass
D3V3, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               0                 5
  CLUS_3               2                 5
D3V4, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2                 5
  CLUS_2               0                 5
  CLUS_3               1                 8
D3V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3    0
  3P GAIN WILD-TYPE   24   16
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3                24
  CLUS_2               0                16
D3V6, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               0                14
  CLUS_2               0                 3
  CLUS_3               3                23
D3V7, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    2
  3P GAIN WILD-TYPE   20   22
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                20
  CLUS_2               2                22
D3V8, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                17
  CLUS_2               2                 7
  CLUS_3               0                18

Clustering(4) Variable = 3q gain mutation analysis
D4V1, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               1                12
  CLUS_3               1                18
D4V2, multiclass
D4V3, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               0                 5
  CLUS_3               2                 5
D4V4, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               2                 5
  CLUS_2               0                 5
  CLUS_3               1                 8
D4V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3    0
  3Q GAIN WILD-TYPE   24   16
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                24
  CLUS_2               0                16
D4V6, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               0                14
  CLUS_2               0                 3
  CLUS_3               3                23
D4V7, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      1    2
  3Q GAIN WILD-TYPE   20   22
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               1                20
  CLUS_2               2                22
D4V8, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               1                17
  CLUS_2               2                 7
  CLUS_3               0                18

Clustering(5) Variable = 4p gain mutation analysis
D5V1, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0                14
  CLUS_2               1                12
  CLUS_3               2                17
D5V2, multiclass
D5V3, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                20 
       TCGA-BF-A1PU        TCGA-BF-A1PX        TCGA-D9-A1X3        TCGA-EB-A1NK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EB-A24C        TCGA-EB-A24D        TCGA-EB-A299        TCGA-ER-A194 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A196        TCGA-ER-A19K        TCGA-ER-A19T        TCGA-ER-A2NB 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A2NF        TCGA-FS-A1ZN        TCGA-GF-A2C7        TCGA-GN-A263 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A269        TCGA-GN-A26C        TCGA-HR-A2OG        TCGA-HR-A2OH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D5V4, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                20 
       TCGA-BF-A1PU        TCGA-BF-A1PX        TCGA-D9-A1X3        TCGA-EB-A1NK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EB-A24C        TCGA-EB-A24D        TCGA-EB-A299        TCGA-ER-A194 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A196        TCGA-ER-A19K        TCGA-ER-A19T        TCGA-ER-A2NB 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A2NF        TCGA-FS-A1ZN        TCGA-GF-A2C7        TCGA-GN-A263 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A269        TCGA-GN-A26C        TCGA-HR-A2OG        TCGA-HR-A2OH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D5V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      3    0
  4P GAIN WILD-TYPE   24   16
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               3                24
  CLUS_2               0                16
D5V6, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0                14
  CLUS_2               0                 3
  CLUS_3               3                23
D5V7, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    2
  4P GAIN WILD-TYPE   20   22
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               1                20
  CLUS_2               2                22
D5V8, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               1                17
  CLUS_2               1                 8
  CLUS_3               1                17

Clustering(6) Variable = 5p gain mutation analysis
D6V1, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               3                10
  CLUS_3               3                16
D6V2, multiclass
D6V3, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               1                 4
  CLUS_3               2                 5
D6V4, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                 5
  CLUS_2               1                 4
  CLUS_3               0                 9
D6V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      4    3
  5P GAIN WILD-TYPE   23   13
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               4                23
  CLUS_2               3                13
D6V6, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               3                11
  CLUS_2               0                 3
  CLUS_3               4                22
D6V7, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      3    4
  5P GAIN WILD-TYPE   18   20
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               3                18
  CLUS_2               4                20
D6V8, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               3                15
  CLUS_2               2                 7
  CLUS_3               2                16

Clustering(7) Variable = 5q gain mutation analysis
D7V1, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               0                14
  CLUS_2               1                12
  CLUS_3               2                17
D7V2, multiclass
D7V3, multiclass
[1] "Remove cluster labels:" "5Q GAIN MUTATED"       
clus
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2                19 
       TCGA-BF-A1PU        TCGA-BF-A1PX        TCGA-BF-A1PZ        TCGA-D9-A1X3 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EB-A24C        TCGA-EB-A24D        TCGA-EB-A299        TCGA-ER-A194 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-ER-A196        TCGA-ER-A19K        TCGA-ER-A2NB        TCGA-ER-A2NF 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        TCGA-GF-A2C7        TCGA-GN-A263        TCGA-GN-A269 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A26C        TCGA-HR-A2OG        TCGA-HR-A2OH 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
D7V4, multiclass
[1] "Remove cluster labels:" "5Q GAIN MUTATED"       
clus
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2                19 
       TCGA-BF-A1PU        TCGA-BF-A1PX        TCGA-BF-A1PZ        TCGA-D9-A1X3 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EB-A24C        TCGA-EB-A24D        TCGA-EB-A299        TCGA-ER-A194 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-ER-A196        TCGA-ER-A19K        TCGA-ER-A2NB        TCGA-ER-A2NF 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        TCGA-GF-A2C7        TCGA-GN-A263        TCGA-GN-A269 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A26C        TCGA-HR-A2OG        TCGA-HR-A2OH 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
D7V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      2    1
  5Q GAIN WILD-TYPE   25   15
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                25
  CLUS_2               1                15
D7V6, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               0                 3
  CLUS_3               2                24
D7V7, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1    2
  5Q GAIN WILD-TYPE   20   22
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1                20
  CLUS_2               2                22
D7V8, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               1                 8
  CLUS_3               0                18

Clustering(8) Variable = 6p gain mutation analysis
D8V1, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               7                 6
  CLUS_3               6                13
D8V2, multiclass
D8V3, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               3                 6
  CLUS_2               2                 3
  CLUS_3               2                 5
D8V4, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2                 5
  CLUS_2               2                 3
  CLUS_3               3                 6
D8V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      7    5
  6P GAIN WILD-TYPE   20   11
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               7                20
  CLUS_2               5                11
D8V6, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               4                10
  CLUS_2               2                 1
  CLUS_3               6                20
D8V7, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      9    4
  6P GAIN WILD-TYPE   12   20
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               9                12
  CLUS_2               4                20
D8V8, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               8                10
  CLUS_2               1                 8
  CLUS_3               4                14

Clustering(9) Variable = 6q gain mutation analysis
D9V1, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               0                14
  CLUS_2               2                11
  CLUS_3               1                18
D9V2, multiclass
D9V3, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                19 
       TCGA-BF-A1PU        TCGA-BF-A1PX        TCGA-BF-A1PZ        TCGA-D9-A1X3 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EB-A1NK        TCGA-EB-A24C        TCGA-EB-A24D        TCGA-EB-A299 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A194        TCGA-ER-A196        TCGA-ER-A19K        TCGA-ER-A19T 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A2NB        TCGA-ER-A2NF        TCGA-GF-A2C7        TCGA-GN-A263 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A26C        TCGA-HR-A2OG        TCGA-HR-A2OH 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D9V4, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                19 
       TCGA-BF-A1PU        TCGA-BF-A1PX        TCGA-BF-A1PZ        TCGA-D9-A1X3 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EB-A1NK        TCGA-EB-A24C        TCGA-EB-A24D        TCGA-EB-A299 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A194        TCGA-ER-A196        TCGA-ER-A19K        TCGA-ER-A19T 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A2NB        TCGA-ER-A2NF        TCGA-GF-A2C7        TCGA-GN-A263 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A26C        TCGA-HR-A2OG        TCGA-HR-A2OH 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D9V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0    2
  6Q GAIN WILD-TYPE   27   14
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               0                27
  CLUS_2               2                14
D9V6, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                41 
       TCGA-BF-A1PU        TCGA-BF-A1PV        TCGA-BF-A1PX        TCGA-BF-A1PZ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BF-A1Q0        TCGA-BF-A3DJ        TCGA-BF-A3DL        TCGA-BF-A3DM 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BF-A3DN        TCGA-D9-A1X3        TCGA-D9-A3Z4        TCGA-D9-A4Z2 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EB-A1NK        TCGA-EB-A24C        TCGA-EB-A24D        TCGA-EB-A299 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC        TCGA-EB-A3XD 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EB-A3XE        TCGA-EB-A3Y6        TCGA-EB-A3Y7        TCGA-EB-A41A 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EB-A41B        TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EB-A430 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A194        TCGA-ER-A196        TCGA-ER-A19K        TCGA-ER-A19T 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A2NF        TCGA-ER-A42H        TCGA-FR-A2OS        TCGA-FR-A3R1 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GF-A2C7        TCGA-GN-A263        TCGA-GN-A26C        TCGA-HR-A2OG 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HR-A2OH 
"6Q GAIN WILD-TYPE" 
D9V7, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2    0
  6Q GAIN WILD-TYPE   19   24
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               2                19
  CLUS_2               0                24
D9V8, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                43 
       TCGA-BF-A1PU        TCGA-BF-A1PV        TCGA-BF-A1PX        TCGA-BF-A1PZ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BF-A1Q0        TCGA-BF-A3DJ        TCGA-BF-A3DL        TCGA-BF-A3DM 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BF-A3DN        TCGA-D9-A1X3        TCGA-D9-A3Z4        TCGA-D9-A4Z2 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EB-A1NK        TCGA-EB-A24C        TCGA-EB-A24D        TCGA-EB-A299 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC        TCGA-EB-A3XD 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EB-A3XE        TCGA-EB-A3Y6        TCGA-EB-A3Y7        TCGA-EB-A41A 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EB-A41B        TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EB-A430 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A194        TCGA-ER-A196        TCGA-ER-A19K        TCGA-ER-A19T 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A2NB        TCGA-ER-A2NF        TCGA-ER-A42H        TCGA-FR-A2OS 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FR-A3R1        TCGA-GF-A2C7        TCGA-GN-A263        TCGA-GN-A26C 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HR-A2OG        TCGA-HR-A2OH        TCGA-IH-A3EA 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 

Clustering(10) Variable = 7p gain mutation analysis
D10V1, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               6                 8
  CLUS_2               6                 7
  CLUS_3               7                12
D10V2, multiclass
D10V3, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               3                 6
  CLUS_2               1                 4
  CLUS_3               5                 2
D10V4, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               5                 2
  CLUS_2               1                 4
  CLUS_3               3                 6
D10V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     11    6
  7P GAIN WILD-TYPE   16   10
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              11                16
  CLUS_2               6                10
D10V6, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               5                 9
  CLUS_2               1                 2
  CLUS_3              11                15
D10V7, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      7   11
  7P GAIN WILD-TYPE   14   13
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               7                14
  CLUS_2              11                13
D10V8, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               7                11
  CLUS_2               5                 4
  CLUS_3               6                12

Clustering(11) Variable = 7q gain mutation analysis
D11V1, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               6                 8
  CLUS_2               6                 7
  CLUS_3               6                13
D11V2, multiclass
D11V3, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               3                 6
  CLUS_2               1                 4
  CLUS_3               4                 3
D11V4, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               4                 3
  CLUS_2               1                 4
  CLUS_3               3                 6
D11V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     11    6
  7Q GAIN WILD-TYPE   16   10
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              11                16
  CLUS_2               6                10
D11V6, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               5                 9
  CLUS_2               1                 2
  CLUS_3              11                15
D11V7, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      7   10
  7Q GAIN WILD-TYPE   14   14
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               7                14
  CLUS_2              10                14
D11V8, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               7                11
  CLUS_2               4                 5
  CLUS_3               6                12

Clustering(12) Variable = 8p gain mutation analysis
D12V1, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               4                 9
  CLUS_3               2                17
D12V2, multiclass
D12V3, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               3                 6
  CLUS_2               1                 4
  CLUS_3               0                 7
D12V4, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               1                 4
  CLUS_3               3                 6
D12V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      5    2
  8P GAIN WILD-TYPE   22   14
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               5                22
  CLUS_2               2                14
D12V6, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               1                 2
  CLUS_3               5                21
D12V7, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3    4
  8P GAIN WILD-TYPE   18   20
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               3                18
  CLUS_2               4                20
D12V8, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               3                15
  CLUS_2               3                 6
  CLUS_3               1                17

Clustering(13) Variable = 8q gain mutation analysis
D13V1, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               3                11
  CLUS_2              10                 3
  CLUS_3               2                17
D13V2, multiclass
D13V3, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               3                 6
  CLUS_2               1                 4
  CLUS_3               1                 6
D13V4, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               1                 4
  CLUS_3               3                 6
D13V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      9    6
  8Q GAIN WILD-TYPE   18   10
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               9                18
  CLUS_2               6                10
D13V6, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               4                10
  CLUS_2               2                 1
  CLUS_3               9                17
D13V7, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      8    7
  8Q GAIN WILD-TYPE   13   17
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               8                13
  CLUS_2               7                17
D13V8, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               7                11
  CLUS_2               3                 6
  CLUS_3               5                13

Clustering(14) Variable = 13q gain mutation analysis
D14V1, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                2                 11
  CLUS_3                0                 19
D14V2, multiclass
D14V3, multiclass
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 2                 19 
        TCGA-BF-A1PU         TCGA-BF-A1PX         TCGA-BF-A1PZ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D9-A1X3         TCGA-EB-A1NK         TCGA-EB-A299 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ER-A194         TCGA-ER-A196         TCGA-ER-A19K 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ER-A19T         TCGA-ER-A2NB         TCGA-ER-A2NF 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZN         TCGA-GF-A2C7         TCGA-GN-A263 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A269         TCGA-GN-A26C         TCGA-HR-A2OG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HR-A2OH 
"13Q GAIN WILD-TYPE" 
D14V4, multiclass
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 2                 19 
        TCGA-BF-A1PU         TCGA-BF-A1PX         TCGA-BF-A1PZ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D9-A1X3         TCGA-EB-A1NK         TCGA-EB-A299 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ER-A194         TCGA-ER-A196         TCGA-ER-A19K 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ER-A19T         TCGA-ER-A2NB         TCGA-ER-A2NF 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZN         TCGA-GF-A2C7         TCGA-GN-A263 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A269         TCGA-GN-A26C         TCGA-HR-A2OG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HR-A2OH 
"13Q GAIN WILD-TYPE" 
D14V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2    2
  13Q GAIN WILD-TYPE   25   14
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                2                 25
  CLUS_2                2                 14
D14V6, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                  2
  CLUS_3                2                 24
D14V7, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3    1
  13Q GAIN WILD-TYPE   18   23
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                 18
  CLUS_2                1                 23
D14V8, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                1                  8
  CLUS_3                2                 16

Clustering(15) Variable = 18p gain mutation analysis
D15V1, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                2                 11
  CLUS_3                4                 15
D15V2, multiclass
D15V3, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                1                  4
  CLUS_3                2                  5
D15V4, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                2                  5
  CLUS_2                1                  4
  CLUS_3                1                  8
D15V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      7    0
  18P GAIN WILD-TYPE   20   16
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                7                 20
  CLUS_2                0                 16
D15V6, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                0                  3
  CLUS_3                7                 19
D15V7, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3    4
  18P GAIN WILD-TYPE   18   20
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                3                 18
  CLUS_2                4                 20
D15V8, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                2                  7
  CLUS_3                3                 15

Clustering(16) Variable = 18q gain mutation analysis
D16V1, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                3                 10
  CLUS_3                4                 15
D16V2, multiclass
D16V3, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                1                  4
  CLUS_3                2                  5
D16V4, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                  5
  CLUS_2                1                  4
  CLUS_3                0                  9
D16V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      6    1
  18Q GAIN WILD-TYPE   21   15
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                6                 21
  CLUS_2                1                 15
D16V6, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                0                  3
  CLUS_3                6                 20
D16V7, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3    5
  18Q GAIN WILD-TYPE   18   19
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                3                 18
  CLUS_2                5                 19
D16V8, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                1                  8
  CLUS_3                4                 14

Clustering(17) Variable = 20p gain mutation analysis
D17V1, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                1                 12
  CLUS_3                5                 14
D17V2, multiclass
D17V3, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                4                  5
  CLUS_2                1                  4
  CLUS_3                1                  6
D17V4, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                1                  4
  CLUS_3                4                  5
D17V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      7    2
  20P GAIN WILD-TYPE   20   14
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                7                 20
  CLUS_2                2                 14
D17V6, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                2                  1
  CLUS_3                6                 20
D17V7, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      3    6
  20P GAIN WILD-TYPE   18   18
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                3                 18
  CLUS_2                6                 18
D17V8, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                1                  8
  CLUS_3                5                 13

Clustering(18) Variable = 20q gain mutation analysis
D18V1, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                4                 10
  CLUS_2                1                 12
  CLUS_3                6                 13
D18V2, multiclass
D18V3, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                4                  5
  CLUS_2                1                  4
  CLUS_3                1                  6
D18V4, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                1                  4
  CLUS_3                4                  5
D18V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      8    3
  20Q GAIN WILD-TYPE   19   13
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                8                 19
  CLUS_2                3                 13
D18V6, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                2                  1
  CLUS_3                7                 19
D18V7, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      4    7
  20Q GAIN WILD-TYPE   17   17
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                4                 17
  CLUS_2                7                 17
D18V8, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                2                  7
  CLUS_3                6                 12

Clustering(19) Variable = 21q gain mutation analysis
D19V1, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                1                 12
  CLUS_3                2                 17
D19V2, multiclass
D19V3, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                 20 
        TCGA-BF-A1PU         TCGA-BF-A1PX         TCGA-BF-A1PZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D9-A1X3         TCGA-EB-A1NK         TCGA-EB-A24C 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EB-A24D         TCGA-EB-A299         TCGA-ER-A194 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A196         TCGA-ER-A19K         TCGA-ER-A19T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A2NB         TCGA-FS-A1ZN         TCGA-GF-A2C7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A263         TCGA-GN-A269         TCGA-GN-A26C 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-HR-A2OG         TCGA-HR-A2OH 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D19V4, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                 20 
        TCGA-BF-A1PU         TCGA-BF-A1PX         TCGA-BF-A1PZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D9-A1X3         TCGA-EB-A1NK         TCGA-EB-A24C 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EB-A24D         TCGA-EB-A299         TCGA-ER-A194 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A196         TCGA-ER-A19K         TCGA-ER-A19T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A2NB         TCGA-FS-A1ZN         TCGA-GF-A2C7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A263         TCGA-GN-A269         TCGA-GN-A26C 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-HR-A2OG         TCGA-HR-A2OH 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D19V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2    1
  21Q GAIN WILD-TYPE   25   15
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                2                 25
  CLUS_2                1                 15
D19V6, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                1                  2
  CLUS_3                2                 24
D19V7, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0    3
  21Q GAIN WILD-TYPE   21   21
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                 21
  CLUS_2                3                 21
D19V8, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                0                  9
  CLUS_3                1                 17

Clustering(20) Variable = 22q gain mutation analysis
D20V1, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                1                 12
  CLUS_3                2                 17
D20V2, multiclass
D20V3, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                3                  6
  CLUS_2                0                  5
  CLUS_3                0                  7
D20V4, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                0                  5
  CLUS_3                3                  6
D20V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2    2
  22Q GAIN WILD-TYPE   25   14
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                2                 25
  CLUS_2                2                 14
D20V6, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                  2
  CLUS_3                2                 24
D20V7, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2    3
  22Q GAIN WILD-TYPE   19   21
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                2                 19
  CLUS_2                3                 21
D20V8, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                1                  8
  CLUS_3                1                 17

Clustering(21) Variable = 2p loss mutation analysis
D21V1, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               4                10
  CLUS_2               1                12
  CLUS_3               0                19
D21V2, multiclass
D21V3, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               4                 5
  CLUS_2               0                 5
  CLUS_3               0                 7
D21V4, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               0                 5
  CLUS_3               4                 5
D21V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3    2
  2P LOSS WILD-TYPE   24   14
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               3                24
  CLUS_2               2                14
D21V6, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               1                 2
  CLUS_3               3                23
D21V7, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3    2
  2P LOSS WILD-TYPE   18   22
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               3                18
  CLUS_2               2                22
D21V8, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               0                 9
  CLUS_3               2                16

Clustering(22) Variable = 2q loss mutation analysis
D22V1, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               3                11
  CLUS_2               1                12
  CLUS_3               0                19
D22V2, multiclass
D22V3, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               3                 6
  CLUS_2               0                 5
  CLUS_3               0                 7
D22V4, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               0                 5
  CLUS_3               3                 6
D22V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2    2
  2Q LOSS WILD-TYPE   25   14
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               2                25
  CLUS_2               2                14
D22V6, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               1                 2
  CLUS_3               2                24
D22V7, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      3    1
  2Q LOSS WILD-TYPE   18   23
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               3                18
  CLUS_2               1                23
D22V8, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               2                16
  CLUS_2               0                 9
  CLUS_3               2                16

Clustering(23) Variable = 4p loss mutation analysis
D23V1, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               3                11
  CLUS_2               1                12
  CLUS_3               3                16
D23V2, multiclass
D23V3, multiclass
[1] "Remove cluster labels:" "4P LOSS MUTATED"       
clus
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                19 
       TCGA-BF-A1PX        TCGA-BF-A1PZ        TCGA-D9-A1X3        TCGA-EB-A1NK 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EB-A24C        TCGA-EB-A24D        TCGA-EB-A299        TCGA-ER-A194 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-ER-A196        TCGA-ER-A19K        TCGA-ER-A2NB        TCGA-ER-A2NF 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        TCGA-GF-A2C7        TCGA-GN-A263        TCGA-GN-A269 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A26C        TCGA-HR-A2OG        TCGA-HR-A2OH 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
D23V4, multiclass
[1] "Remove cluster labels:" "4P LOSS MUTATED"       
clus
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                19 
       TCGA-BF-A1PX        TCGA-BF-A1PZ        TCGA-D9-A1X3        TCGA-EB-A1NK 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EB-A24C        TCGA-EB-A24D        TCGA-EB-A299        TCGA-ER-A194 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-ER-A196        TCGA-ER-A19K        TCGA-ER-A2NB        TCGA-ER-A2NF 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        TCGA-GF-A2C7        TCGA-GN-A263        TCGA-GN-A269 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A26C        TCGA-HR-A2OG        TCGA-HR-A2OH 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
D23V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      5    2
  4P LOSS WILD-TYPE   22   14
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               5                22
  CLUS_2               2                14
D23V6, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               2                12
  CLUS_2               0                 3
  CLUS_3               5                21
D23V7, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      4    3
  4P LOSS WILD-TYPE   17   21
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               4                17
  CLUS_2               3                21
D23V8, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               1                 8
  CLUS_3               3                15

Clustering(24) Variable = 4q loss mutation analysis
D24V1, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               5                 9
  CLUS_2               1                12
  CLUS_3               3                16
D24V2, multiclass
D24V3, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               0                 5
  CLUS_3               1                 6
D24V4, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               0                 5
  CLUS_3               2                 7
D24V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      6    3
  4Q LOSS WILD-TYPE   21   13
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               6                21
  CLUS_2               3                13
D24V6, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               3                11
  CLUS_2               0                 3
  CLUS_3               6                20
D24V7, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      6    3
  4Q LOSS WILD-TYPE   15   21
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               6                15
  CLUS_2               3                21
D24V8, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               4                14
  CLUS_2               1                 8
  CLUS_3               4                14

Clustering(25) Variable = 5q loss mutation analysis
D25V1, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               3                11
  CLUS_2               2                11
  CLUS_3               1                18
D25V2, multiclass
D25V3, multiclass
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
clus
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                2                19 
       TCGA-BF-A1PU        TCGA-BF-A1PX        TCGA-BF-A1PZ        TCGA-EB-A1NK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EB-A24C        TCGA-EB-A24D        TCGA-EB-A299        TCGA-ER-A194 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ER-A196        TCGA-ER-A19K        TCGA-ER-A19T        TCGA-ER-A2NB 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ER-A2NF        TCGA-FS-A1ZN        TCGA-GF-A2C7        TCGA-GN-A269 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A26C        TCGA-HR-A2OG        TCGA-HR-A2OH 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
D25V4, multiclass
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
clus
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                2                19 
       TCGA-BF-A1PU        TCGA-BF-A1PX        TCGA-BF-A1PZ        TCGA-EB-A1NK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EB-A24C        TCGA-EB-A24D        TCGA-EB-A299        TCGA-ER-A194 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ER-A196        TCGA-ER-A19K        TCGA-ER-A19T        TCGA-ER-A2NB 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ER-A2NF        TCGA-FS-A1ZN        TCGA-GF-A2C7        TCGA-GN-A269 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A26C        TCGA-HR-A2OG        TCGA-HR-A2OH 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
D25V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      4    2
  5Q LOSS WILD-TYPE   23   14
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               4                23
  CLUS_2               2                14
D25V6, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               2                12
  CLUS_2               0                 3
  CLUS_3               4                22
D25V7, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      2    4
  5Q LOSS WILD-TYPE   19   20
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               2                19
  CLUS_2               4                20
D25V8, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               2                 7
  CLUS_3               3                15

Clustering(26) Variable = 6q loss mutation analysis
D26V1, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               2                12
  CLUS_2               8                 5
  CLUS_3               5                14
D26V2, multiclass
D26V3, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               0                 5
  CLUS_3               3                 4
D26V4, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               3                 4
  CLUS_2               0                 5
  CLUS_3               2                 7
D26V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      9    4
  6Q LOSS WILD-TYPE   18   12
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               9                18
  CLUS_2               4                12
D26V6, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               2                12
  CLUS_2               2                 1
  CLUS_3               9                17
D26V7, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      6    9
  6Q LOSS WILD-TYPE   15   15
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               6                15
  CLUS_2               9                15
D26V8, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               6                12
  CLUS_2               4                 5
  CLUS_3               5                13

Clustering(27) Variable = 8p loss mutation analysis
D27V1, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               4                10
  CLUS_2               5                 8
  CLUS_3               2                17
D27V2, multiclass
D27V3, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               0                 5
  CLUS_3               2                 5
D27V4, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               2                 5
  CLUS_2               0                 5
  CLUS_3               2                 7
D27V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      5    5
  8P LOSS WILD-TYPE   22   11
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               5                22
  CLUS_2               5                11
D27V6, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               4                10
  CLUS_2               1                 2
  CLUS_3               5                21
D27V7, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      5    6
  8P LOSS WILD-TYPE   16   18
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               5                16
  CLUS_2               6                18
D27V8, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               7                11
  CLUS_2               1                 8
  CLUS_3               3                15

Clustering(28) Variable = 8q loss mutation analysis
D28V1, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               4                10
  CLUS_2               1                12
  CLUS_3               0                19
D28V2, multiclass
D28V3, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                19 
       TCGA-BF-A1PU        TCGA-BF-A1PX        TCGA-BF-A1PZ        TCGA-D9-A1X3 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EB-A1NK        TCGA-EB-A24D        TCGA-EB-A299        TCGA-ER-A194 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ER-A196        TCGA-ER-A19K        TCGA-ER-A2NB        TCGA-ER-A2NF 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        TCGA-GF-A2C7        TCGA-GN-A263        TCGA-GN-A269 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GN-A26C        TCGA-HR-A2OG        TCGA-HR-A2OH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D28V4, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                19 
       TCGA-BF-A1PU        TCGA-BF-A1PX        TCGA-BF-A1PZ        TCGA-D9-A1X3 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EB-A1NK        TCGA-EB-A24D        TCGA-EB-A299        TCGA-ER-A194 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ER-A196        TCGA-ER-A19K        TCGA-ER-A2NB        TCGA-ER-A2NF 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        TCGA-GF-A2C7        TCGA-GN-A263        TCGA-GN-A269 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GN-A26C        TCGA-HR-A2OG        TCGA-HR-A2OH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D28V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3    2
  8Q LOSS WILD-TYPE   24   14
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               3                24
  CLUS_2               2                14
D28V6, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               2                12
  CLUS_2               0                 3
  CLUS_3               3                23
D28V7, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3    2
  8Q LOSS WILD-TYPE   18   22
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               3                18
  CLUS_2               2                22
D28V8, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               1                 8
  CLUS_3               1                17

Clustering(29) Variable = 9p loss mutation analysis
D29V1, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              11                 3
  CLUS_2               9                 4
  CLUS_3               5                14
D29V2, multiclass
D29V3, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               3                 6
  CLUS_2               3                 2
  CLUS_3               1                 6
D29V4, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               3                 2
  CLUS_3               3                 6
D29V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     16    9
  9P LOSS WILD-TYPE   11    7
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              16                11
  CLUS_2               9                 7
D29V6, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               8                 6
  CLUS_2               1                 2
  CLUS_3              16                10
D29V7, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     16    9
  9P LOSS WILD-TYPE    5   15
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              16                 5
  CLUS_2               9                15
D29V8, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               7                11
  CLUS_2               3                 6
  CLUS_3              15                 3

Clustering(30) Variable = 9q loss mutation analysis
D30V1, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               6                 8
  CLUS_2               5                 8
  CLUS_3               4                15
D30V2, multiclass
D30V3, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               1                 4
  CLUS_3               1                 6
D30V4, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               1                 4
  CLUS_3               1                 8
D30V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     10    5
  9Q LOSS WILD-TYPE   17   11
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              10                17
  CLUS_2               5                11
D30V6, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               5                 9
  CLUS_2               0                 3
  CLUS_3              10                16
D30V7, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      9    6
  9Q LOSS WILD-TYPE   12   18
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               9                12
  CLUS_2               6                18
D30V8, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               2                 7
  CLUS_3              10                 8

Clustering(31) Variable = 10p loss mutation analysis
D31V1, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               11                  3
  CLUS_2                6                  7
  CLUS_3                2                 17
D31V2, multiclass
D31V3, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                6                  3
  CLUS_2                1                  4
  CLUS_3                1                  6
D31V4, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                1                  4
  CLUS_3                6                  3
D31V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     12    7
  10P LOSS WILD-TYPE   15    9
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               12                 15
  CLUS_2                7                  9
D31V6, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                6                  8
  CLUS_2                1                  2
  CLUS_3               12                 14
D31V7, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     12    7
  10P LOSS WILD-TYPE    9   17
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               12                  9
  CLUS_2                7                 17
D31V8, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                7                 11
  CLUS_2                4                  5
  CLUS_3                8                 10

Clustering(32) Variable = 10q loss mutation analysis
D32V1, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               12                  2
  CLUS_2                8                  5
  CLUS_3                2                 17
D32V2, multiclass
D32V3, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                6                  3
  CLUS_2                1                  4
  CLUS_3                1                  6
D32V4, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                1                  4
  CLUS_3                6                  3
D32V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     13    9
  10Q LOSS WILD-TYPE   14    7
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               13                 14
  CLUS_2                9                  7
D32V6, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                8                  6
  CLUS_2                1                  2
  CLUS_3               13                 13
D32V7, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     14    8
  10Q LOSS WILD-TYPE    7   16
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               14                  7
  CLUS_2                8                 16
D32V8, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                7                 11
  CLUS_2                4                  5
  CLUS_3               11                  7

Clustering(33) Variable = 11p loss mutation analysis
D33V1, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                4                  9
  CLUS_3                3                 16
D33V2, multiclass
D33V3, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                2                  7
  CLUS_2                1                  4
  CLUS_3                0                  7
D33V4, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                1                  4
  CLUS_3                2                  7
D33V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      6    2
  11P LOSS WILD-TYPE   21   14
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                6                 21
  CLUS_2                2                 14
D33V6, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                  2
  CLUS_3                6                 20
D33V7, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      5    3
  11P LOSS WILD-TYPE   16   21
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                5                 16
  CLUS_2                3                 21
D33V8, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                5                 13
  CLUS_2                1                  8
  CLUS_3                2                 16

Clustering(34) Variable = 11q loss mutation analysis
D34V1, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                5                  8
  CLUS_3                4                 15
D34V2, multiclass
D34V3, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                  7
  CLUS_2                1                  4
  CLUS_3                1                  6
D34V4, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                1                  4
  CLUS_3                2                  7
D34V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      8    2
  11Q LOSS WILD-TYPE   19   14
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                8                 19
  CLUS_2                2                 14
D34V6, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                  2
  CLUS_3                8                 18
D34V7, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      6    4
  11Q LOSS WILD-TYPE   15   20
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                6                 15
  CLUS_2                4                 20
D34V8, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                5                 13
  CLUS_2                2                  7
  CLUS_3                3                 15

Clustering(35) Variable = 12p loss mutation analysis
D35V1, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                2                 11
  CLUS_3                2                 17
D35V2, multiclass
D35V3, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                3                  6
  CLUS_2                0                  5
  CLUS_3                0                  7
D35V4, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                0                  5
  CLUS_3                3                  6
D35V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      5    1
  12P LOSS WILD-TYPE   22   15
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                5                 22
  CLUS_2                1                 15
D35V6, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                1                  2
  CLUS_3                5                 21
D35V7, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      4    2
  12P LOSS WILD-TYPE   17   22
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                4                 17
  CLUS_2                2                 22
D35V8, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                1                  8
  CLUS_3                4                 14

Clustering(36) Variable = 12q loss mutation analysis
D36V1, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                2                 11
  CLUS_3                3                 16
D36V2, multiclass
D36V3, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                3                  6
  CLUS_2                0                  5
  CLUS_3                1                  6
D36V4, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                0                  5
  CLUS_3                3                  6
D36V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      5    3
  12Q LOSS WILD-TYPE   22   13
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                5                 22
  CLUS_2                3                 13
D36V6, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                1                  2
  CLUS_3                5                 21
D36V7, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      5    3
  12Q LOSS WILD-TYPE   16   21
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                5                 16
  CLUS_2                3                 21
D36V8, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                1                  8
  CLUS_3                5                 13

Clustering(37) Variable = 13q loss mutation analysis
D37V1, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                1                 12
  CLUS_3                4                 15
D37V2, multiclass
D37V3, multiclass
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                 19 
        TCGA-BF-A1PU         TCGA-BF-A1PX         TCGA-BF-A1PZ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D9-A1X3         TCGA-EB-A1NK         TCGA-EB-A24C 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EB-A24D         TCGA-EB-A299         TCGA-ER-A194 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A196         TCGA-ER-A19K         TCGA-ER-A2NB 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A2NF         TCGA-FS-A1ZN         TCGA-GF-A2C7 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A263         TCGA-GN-A269         TCGA-HR-A2OG 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-HR-A2OH 
"13Q LOSS WILD-TYPE" 
D37V4, multiclass
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                 19 
        TCGA-BF-A1PU         TCGA-BF-A1PX         TCGA-BF-A1PZ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D9-A1X3         TCGA-EB-A1NK         TCGA-EB-A24C 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EB-A24D         TCGA-EB-A299         TCGA-ER-A194 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A196         TCGA-ER-A19K         TCGA-ER-A2NB 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A2NF         TCGA-FS-A1ZN         TCGA-GF-A2C7 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A263         TCGA-GN-A269         TCGA-HR-A2OG 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-HR-A2OH 
"13Q LOSS WILD-TYPE" 
D37V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      6    1
  13Q LOSS WILD-TYPE   21   15
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                6                 21
  CLUS_2                1                 15
D37V6, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                0                  3
  CLUS_3                6                 20
D37V7, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4    3
  13Q LOSS WILD-TYPE   17   21
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                4                 17
  CLUS_2                3                 21
D37V8, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                3                  6
  CLUS_3                2                 16

Clustering(38) Variable = 14q loss mutation analysis
D38V1, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                4                  9
  CLUS_3                0                 19
D38V2, multiclass
D38V3, multiclass
[1] "Remove cluster labels:" "14Q LOSS MUTATED"      
clus
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 1                 20 
        TCGA-BF-A1PU         TCGA-BF-A1PX         TCGA-BF-A1PZ 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D9-A1X3         TCGA-EB-A1NK         TCGA-EB-A24C 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EB-A299         TCGA-ER-A194         TCGA-ER-A196 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A19K         TCGA-ER-A19T         TCGA-ER-A2NB 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A2NF         TCGA-FS-A1ZN         TCGA-GF-A2C7 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-GN-A263         TCGA-GN-A269         TCGA-GN-A26C 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-HR-A2OG         TCGA-HR-A2OH 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
D38V4, multiclass
[1] "Remove cluster labels:" "14Q LOSS MUTATED"      
clus
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 1                 20 
        TCGA-BF-A1PU         TCGA-BF-A1PX         TCGA-BF-A1PZ 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D9-A1X3         TCGA-EB-A1NK         TCGA-EB-A24C 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EB-A299         TCGA-ER-A194         TCGA-ER-A196 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A19K         TCGA-ER-A19T         TCGA-ER-A2NB 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A2NF         TCGA-FS-A1ZN         TCGA-GF-A2C7 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-GN-A263         TCGA-GN-A269         TCGA-GN-A26C 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-HR-A2OG         TCGA-HR-A2OH 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
D38V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      4    2
  14Q LOSS WILD-TYPE   23   14
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                4                 23
  CLUS_2                2                 14
D38V6, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                  2
  CLUS_3                4                 22
D38V7, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      4    2
  14Q LOSS WILD-TYPE   17   22
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                4                 17
  CLUS_2                2                 22
D38V8, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                1                  8
  CLUS_3                5                 13

Clustering(39) Variable = 16p loss mutation analysis
D39V1, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                1                 12
  CLUS_3                0                 19
D39V2, multiclass
D39V3, multiclass
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 20 
        TCGA-BF-A1PU         TCGA-BF-A1PX         TCGA-BF-A1PZ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D9-A1X3         TCGA-EB-A1NK         TCGA-EB-A24C 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EB-A299         TCGA-ER-A194         TCGA-ER-A196 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A19K         TCGA-ER-A19T         TCGA-ER-A2NB 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A2NF         TCGA-FS-A1ZN         TCGA-GF-A2C7 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A263         TCGA-GN-A269         TCGA-GN-A26C 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HR-A2OG         TCGA-HR-A2OH 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
D39V4, multiclass
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 20 
        TCGA-BF-A1PU         TCGA-BF-A1PX         TCGA-BF-A1PZ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D9-A1X3         TCGA-EB-A1NK         TCGA-EB-A24C 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EB-A299         TCGA-ER-A194         TCGA-ER-A196 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A19K         TCGA-ER-A19T         TCGA-ER-A2NB 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A2NF         TCGA-FS-A1ZN         TCGA-GF-A2C7 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A263         TCGA-GN-A269         TCGA-GN-A26C 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HR-A2OG         TCGA-HR-A2OH 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
D39V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    2
  16P LOSS WILD-TYPE   26   14
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                2                 14
D39V6, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                  2
  CLUS_3                1                 25
D39V7, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2    1
  16P LOSS WILD-TYPE   19   23
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                2                 19
  CLUS_2                1                 23
D39V8, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                1                  8
  CLUS_3                2                 16

Clustering(40) Variable = 16q loss mutation analysis
D40V1, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                4                 10
  CLUS_2                5                  8
  CLUS_3                4                 15
D40V2, multiclass
D40V3, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                2                  7
  CLUS_2                1                  4
  CLUS_3                2                  5
D40V4, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                2                  5
  CLUS_2                1                  4
  CLUS_3                2                  7
D40V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      9    3
  16Q LOSS WILD-TYPE   18   13
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                9                 18
  CLUS_2                3                 13
D40V6, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                2                  1
  CLUS_3                8                 18
D40V7, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      7    5
  16Q LOSS WILD-TYPE   14   19
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                7                 14
  CLUS_2                5                 19
D40V8, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                4                  5
  CLUS_3                5                 13

Clustering(41) Variable = 17p loss mutation analysis
D41V1, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                2                 11
  CLUS_3                3                 16
D41V2, multiclass
D41V3, multiclass
[1] "Remove cluster labels:" "17P LOSS MUTATED"      
clus
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 2                 19 
        TCGA-BF-A1PU         TCGA-BF-A1PX         TCGA-BF-A1PZ 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D9-A1X3         TCGA-EB-A24C         TCGA-EB-A24D 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EB-A299         TCGA-ER-A194         TCGA-ER-A196 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19K         TCGA-ER-A2NB         TCGA-ER-A2NF 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1ZN         TCGA-GF-A2C7         TCGA-GN-A263 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A269         TCGA-GN-A26C         TCGA-HR-A2OG 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-HR-A2OH 
"17P LOSS WILD-TYPE" 
D41V4, multiclass
[1] "Remove cluster labels:" "17P LOSS MUTATED"      
clus
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 2                 19 
        TCGA-BF-A1PU         TCGA-BF-A1PX         TCGA-BF-A1PZ 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D9-A1X3         TCGA-EB-A24C         TCGA-EB-A24D 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EB-A299         TCGA-ER-A194         TCGA-ER-A196 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19K         TCGA-ER-A2NB         TCGA-ER-A2NF 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1ZN         TCGA-GF-A2C7         TCGA-GN-A263 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A269         TCGA-GN-A26C         TCGA-HR-A2OG 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-HR-A2OH 
"17P LOSS WILD-TYPE" 
D41V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      6    2
  17P LOSS WILD-TYPE   21   14
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                6                 21
  CLUS_2                2                 14
D41V6, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                0                  3
  CLUS_3                6                 20
D41V7, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3    5
  17P LOSS WILD-TYPE   18   19
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                3                 18
  CLUS_2                5                 19
D41V8, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                5                 13
  CLUS_2                2                  7
  CLUS_3                1                 17

Clustering(42) Variable = 17q loss mutation analysis
D42V1, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                2                 11
  CLUS_3                0                 19
D42V2, multiclass
D42V3, multiclass
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                 20 
        TCGA-BF-A1PU         TCGA-BF-A1PX         TCGA-BF-A1PZ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D9-A1X3         TCGA-EB-A1NK         TCGA-EB-A24C 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EB-A24D         TCGA-EB-A299         TCGA-ER-A194 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A196         TCGA-ER-A19K         TCGA-ER-A2NB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A2NF         TCGA-FS-A1ZN         TCGA-GF-A2C7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A263         TCGA-GN-A269         TCGA-GN-A26C 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-HR-A2OG         TCGA-HR-A2OH 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
D42V4, multiclass
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                 20 
        TCGA-BF-A1PU         TCGA-BF-A1PX         TCGA-BF-A1PZ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D9-A1X3         TCGA-EB-A1NK         TCGA-EB-A24C 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EB-A24D         TCGA-EB-A299         TCGA-ER-A194 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A196         TCGA-ER-A19K         TCGA-ER-A2NB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A2NF         TCGA-FS-A1ZN         TCGA-GF-A2C7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A263         TCGA-GN-A269         TCGA-GN-A26C 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-HR-A2OG         TCGA-HR-A2OH 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
D42V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4    1
  17Q LOSS WILD-TYPE   23   15
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                4                 23
  CLUS_2                1                 15
D42V6, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                0                  3
  CLUS_3                4                 22
D42V7, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3    2
  17Q LOSS WILD-TYPE   18   22
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                3                 18
  CLUS_2                2                 22
D42V8, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                1                  8
  CLUS_3                1                 17

Clustering(43) Variable = 18p loss mutation analysis
D43V1, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                2                 11
  CLUS_3                1                 18
D43V2, multiclass
D43V3, multiclass
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 2                 19 
        TCGA-BF-A1PU         TCGA-BF-A1PX         TCGA-BF-A1PZ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EB-A1NK         TCGA-EB-A24C         TCGA-EB-A24D 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A194         TCGA-ER-A196         TCGA-ER-A19K 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19T         TCGA-ER-A2NB         TCGA-ER-A2NF 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A1ZN         TCGA-GF-A2C7         TCGA-GN-A263 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A269         TCGA-GN-A26C         TCGA-HR-A2OG 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-HR-A2OH 
"18P LOSS WILD-TYPE" 
D43V4, multiclass
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 2                 19 
        TCGA-BF-A1PU         TCGA-BF-A1PX         TCGA-BF-A1PZ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EB-A1NK         TCGA-EB-A24C         TCGA-EB-A24D 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A194         TCGA-ER-A196         TCGA-ER-A19K 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19T         TCGA-ER-A2NB         TCGA-ER-A2NF 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A1ZN         TCGA-GF-A2C7         TCGA-GN-A263 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A269         TCGA-GN-A26C         TCGA-HR-A2OG 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-HR-A2OH 
"18P LOSS WILD-TYPE" 
D43V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      4    1
  18P LOSS WILD-TYPE   23   15
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                4                 23
  CLUS_2                1                 15
D43V6, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                0                  3
  CLUS_3                4                 22
D43V7, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3    2
  18P LOSS WILD-TYPE   18   22
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                 18
  CLUS_2                2                 22
D43V8, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                1                  8
  CLUS_3                3                 15

Clustering(44) Variable = 18q loss mutation analysis
D44V1, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                1                 12
  CLUS_3                1                 18
D44V2, multiclass
D44V3, multiclass
[1] "Remove cluster labels:" "18Q LOSS MUTATED"      
clus
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 2                 19 
        TCGA-BF-A1PU         TCGA-BF-A1PX         TCGA-BF-A1PZ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EB-A1NK         TCGA-EB-A24C         TCGA-EB-A24D 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A194         TCGA-ER-A196         TCGA-ER-A19K 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19T         TCGA-ER-A2NB         TCGA-ER-A2NF 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZN         TCGA-GF-A2C7         TCGA-GN-A263 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A269         TCGA-GN-A26C         TCGA-HR-A2OG 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-HR-A2OH 
"18Q LOSS WILD-TYPE" 
D44V4, multiclass
[1] "Remove cluster labels:" "18Q LOSS MUTATED"      
clus
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 2                 19 
        TCGA-BF-A1PU         TCGA-BF-A1PX         TCGA-BF-A1PZ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EB-A1NK         TCGA-EB-A24C         TCGA-EB-A24D 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A194         TCGA-ER-A196         TCGA-ER-A19K 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19T         TCGA-ER-A2NB         TCGA-ER-A2NF 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZN         TCGA-GF-A2C7         TCGA-GN-A263 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A269         TCGA-GN-A26C         TCGA-HR-A2OG 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-HR-A2OH 
"18Q LOSS WILD-TYPE" 
D44V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3    1
  18Q LOSS WILD-TYPE   24   15
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                3                 24
  CLUS_2                1                 15
D44V6, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                0                  3
  CLUS_3                3                 23
D44V7, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2    2
  18Q LOSS WILD-TYPE   19   22
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                2                 19
  CLUS_2                2                 22
D44V8, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                1                  8
  CLUS_3                2                 16

Clustering(45) Variable = 19q loss mutation analysis
D45V1, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                0                 13
  CLUS_3                2                 17
D45V2, multiclass
D45V3, multiclass
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 1                 20 
        TCGA-BF-A1PU         TCGA-BF-A1PX         TCGA-BF-A1PZ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D9-A1X3         TCGA-EB-A24C         TCGA-EB-A24D 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EB-A299         TCGA-ER-A194         TCGA-ER-A196 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19K         TCGA-ER-A19T         TCGA-ER-A2NB 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A2NF         TCGA-FS-A1ZN         TCGA-GF-A2C7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A263         TCGA-GN-A269         TCGA-GN-A26C 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-HR-A2OG         TCGA-HR-A2OH 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
D45V4, multiclass
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 1                 20 
        TCGA-BF-A1PU         TCGA-BF-A1PX         TCGA-BF-A1PZ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D9-A1X3         TCGA-EB-A24C         TCGA-EB-A24D 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EB-A299         TCGA-ER-A194         TCGA-ER-A196 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19K         TCGA-ER-A19T         TCGA-ER-A2NB 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A2NF         TCGA-FS-A1ZN         TCGA-GF-A2C7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A263         TCGA-GN-A269         TCGA-GN-A26C 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-HR-A2OG         TCGA-HR-A2OH 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
D45V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    2
  19Q LOSS WILD-TYPE   26   14
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                2                 14
D45V6, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                0                  3
  CLUS_3                1                 25
D45V7, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0    3
  19Q LOSS WILD-TYPE   21   21
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                0                 21
  CLUS_2                3                 21
D45V8, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                1                  8
  CLUS_3                0                 18

Clustering(46) Variable = 21q loss mutation analysis
D46V1, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                3                 10
  CLUS_3                1                 18
D46V2, multiclass
D46V3, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                  7
  CLUS_2                0                  5
  CLUS_3                2                  5
D46V4, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                  5
  CLUS_2                0                  5
  CLUS_3                2                  7
D46V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      2    3
  21Q LOSS WILD-TYPE   25   13
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                 25
  CLUS_2                3                 13
D46V6, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                1                  2
  CLUS_3                2                 24
D46V7, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3    3
  21Q LOSS WILD-TYPE   18   21
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                3                 18
  CLUS_2                3                 21
D46V8, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                2                  7
  CLUS_3                2                 16

Clustering(47) Variable = 22q loss mutation analysis
D47V1, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                 12
  CLUS_3                3                 16
D47V2, multiclass
D47V3, multiclass
[1] "Remove cluster labels:" "22Q LOSS MUTATED"      
clus
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                 20 
        TCGA-BF-A1PU         TCGA-BF-A1PX         TCGA-BF-A1PZ 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D9-A1X3         TCGA-EB-A1NK         TCGA-EB-A24C 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EB-A24D         TCGA-EB-A299         TCGA-ER-A194 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A196         TCGA-ER-A19K         TCGA-ER-A19T 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A2NF         TCGA-FS-A1ZN         TCGA-GF-A2C7 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A263         TCGA-GN-A269         TCGA-GN-A26C 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-HR-A2OG         TCGA-HR-A2OH 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
D47V4, multiclass
[1] "Remove cluster labels:" "22Q LOSS MUTATED"      
clus
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                 20 
        TCGA-BF-A1PU         TCGA-BF-A1PX         TCGA-BF-A1PZ 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D9-A1X3         TCGA-EB-A1NK         TCGA-EB-A24C 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EB-A24D         TCGA-EB-A299         TCGA-ER-A194 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A196         TCGA-ER-A19K         TCGA-ER-A19T 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A2NF         TCGA-FS-A1ZN         TCGA-GF-A2C7 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A263         TCGA-GN-A269         TCGA-GN-A26C 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-HR-A2OG         TCGA-HR-A2OH 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
D47V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      3    1
  22Q LOSS WILD-TYPE   24   15
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                3                 24
  CLUS_2                1                 15
D47V6, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                0                  3
  CLUS_3                3                 23
D47V7, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      2    3
  22Q LOSS WILD-TYPE   19   21
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                2                 19
  CLUS_2                3                 21
D47V8, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                2                  7
  CLUS_3                3                 15
                     V1                      V2                      V3 
              "CN_CNMF"      "METHLYATION_CNMF"             "RPPA_CNMF" 
                     V4                      V5                      V6 
   "RPPA_CHIERARCHICAL"          "MRNASEQ_CNMF" "MRNASEQ_CHIERARCHICAL" 
                     V7                      V8 
          "MIRSEQ_CNMF"  "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
