
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/375842/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/KICH-TP/2907566/1.GDAC_mergedClustering.Finished/KICH-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=KICH-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=KICH-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=66, in cluster file=66, common to both=66
[1] "Reduce the number of clustering variables from 80 to 57."
[1] 57 66
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                5                61 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                5                61 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5                61 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5                61 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               18                48 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               18                48 
[1] "4q gain mutation analysis"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               17                49 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               17                49 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                5                61 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                5                61 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                5                61 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                5                61 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               18                48 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               18                48 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               18                48 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               18                48 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               13                53 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               13                53 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               14                52 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               14                52 
[1] "9p gain mutation analysis"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                8                58 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                8                58 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                8                58 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                8                58 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                13                 53 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                13                 53 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                14                 52 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                14                 52 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                14                 52 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                14                 52 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                13                 53 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                13                 53 
[1] "14q gain mutation analysis"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                16                 50 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                16                 50 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                14                 52 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                14                 52 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                15                 51 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                15                 51 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                15                 51 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                15                 51 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                14                 52 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                14                 52 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                13                 53 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                13                 53 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                11                 55 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                11                 55 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 9                 57 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 9                 57 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                14                 52 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                14                 52 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                15                 51 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                15                 51 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                 63 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                 63 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                15                 51 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                15                 51 
[1] "Xq gain mutation analysis"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                9                57 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                9                57 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               48                18 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               48                18 
[1] "1q loss mutation analysis"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               47                19 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               47                19 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               43                23 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               43                23 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               43                23 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               43                23 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                7                59 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                7                59 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                6                60 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                6                60 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7                59 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7                59 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                7                59 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                7                59 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               47                19 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               47                19 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               47                19 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               47                19 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                9                57 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                9                57 
[1] "8q loss mutation analysis"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                8                58 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                8                58 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                8                58 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                8                58 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                8                58 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                8                58 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                44                 22 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                44                 22 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                44                 22 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                44                 22 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                 61 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                 61 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                 61 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                 61 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                37                 29 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                37                 29 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                 63 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                 63 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 62 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 62 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                45                 21 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                45                 21 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                45                 21 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                45                 21 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                 61 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                 61 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 7                 59 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 7                 59 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                28                 38 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                28                 38 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 5                 61 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 5                 61 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               33                33 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               33                33 
[1] "data2feature, selection=ALL"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 6 rows and 66 columns.

Variable 1:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 66 columns, 0 survival variables, and 6 non-survival variables.
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 3p gain mutation analysis
D1V1, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               5                42
  CLUS_3               0                14
D1V2, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                16
  CLUS_2               2                32
  CLUS_3               2                12
D1V3, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                18
  CLUS_2               2                20
  CLUS_3               1                14
  CLUS_4               1                 9
D1V4, multiclass
D1V5, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3                19
  CLUS_2               2                20
  CLUS_3               0                22
D1V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2    3
  3P GAIN WILD-TYPE    7   54
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               3                54

Clustering(2) Variable = 3q gain mutation analysis
D2V1, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               5                42
  CLUS_3               0                14
D2V2, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               1                16
  CLUS_2               2                32
  CLUS_3               2                12
D2V3, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               1                18
  CLUS_2               2                20
  CLUS_3               1                14
  CLUS_4               1                 9
D2V4, multiclass
D2V5, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                19
  CLUS_2               2                20
  CLUS_3               0                22
D2V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      2    3
  3Q GAIN WILD-TYPE    7   54
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               3                54

Clustering(3) Variable = 4p gain mutation analysis
D3V1, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0                 5
  CLUS_2              13                34
  CLUS_3               5                 9
D3V2, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               4                13
  CLUS_2               9                25
  CLUS_3               5                 9
D3V3, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               3                16
  CLUS_2              14                 8
  CLUS_3               1                14
  CLUS_4               0                10
D3V4, multiclass
D3V5, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               4                18
  CLUS_2               8                14
  CLUS_3               6                16
D3V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0   18
  4P GAIN WILD-TYPE    9   39
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0                 9
  CLUS_2              18                39

Clustering(4) Variable = 4q gain mutation analysis
D4V1, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0                 5
  CLUS_2              12                35
  CLUS_3               5                 9
D4V2, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               4                13
  CLUS_2               8                26
  CLUS_3               5                 9
D4V3, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               3                16
  CLUS_2              13                 9
  CLUS_3               1                14
  CLUS_4               0                10
D4V4, multiclass
D4V5, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               3                19
  CLUS_2               8                14
  CLUS_3               6                16
D4V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0   17
  4Q GAIN WILD-TYPE    9   40
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0                 9
  CLUS_2              17                40

Clustering(5) Variable = 5p gain mutation analysis
D5V1, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               3                44
  CLUS_3               2                12
D5V2, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               1                16
  CLUS_2               2                32
  CLUS_3               2                12
D5V3, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               1                18
  CLUS_2               2                20
  CLUS_3               1                14
  CLUS_4               1                 9
D5V4, multiclass
D5V5, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                20
  CLUS_2               1                21
  CLUS_3               2                20
D5V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2    3
  5P GAIN WILD-TYPE    7   54
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               3                54

Clustering(6) Variable = 5q gain mutation analysis
D6V1, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               3                44
  CLUS_3               2                12
D6V2, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1                16
  CLUS_2               2                32
  CLUS_3               2                12
D6V3, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1                18
  CLUS_2               2                20
  CLUS_3               1                14
  CLUS_4               1                 9
D6V4, multiclass
D6V5, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                20
  CLUS_2               1                21
  CLUS_3               2                20
D6V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      2    3
  5Q GAIN WILD-TYPE    7   54
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               3                54

Clustering(7) Variable = 7p gain mutation analysis
D7V1, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               0                 5
  CLUS_2              13                34
  CLUS_3               5                 9
D7V2, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               4                13
  CLUS_2               8                26
  CLUS_3               6                 8
D7V3, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               3                16
  CLUS_2              12                10
  CLUS_3               2                13
  CLUS_4               1                 9
D7V4, multiclass
D7V5, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               5                17
  CLUS_2               8                14
  CLUS_3               5                17
D7V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      2   16
  7P GAIN WILD-TYPE    7   41
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               2                 7
  CLUS_2              16                41

Clustering(8) Variable = 7q gain mutation analysis
D8V1, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               0                 5
  CLUS_2              13                34
  CLUS_3               5                 9
D8V2, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               4                13
  CLUS_2               8                26
  CLUS_3               6                 8
D8V3, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               3                16
  CLUS_2              12                10
  CLUS_3               2                13
  CLUS_4               1                 9
D8V4, multiclass
D8V5, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               5                17
  CLUS_2               8                14
  CLUS_3               5                17
D8V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2   16
  7Q GAIN WILD-TYPE    7   41
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               2                 7
  CLUS_2              16                41

Clustering(9) Variable = 8p gain mutation analysis
D9V1, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               0                 5
  CLUS_2              12                35
  CLUS_3               1                13
D9V2, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               2                15
  CLUS_2               5                29
  CLUS_3               6                 8
D9V3, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                18
  CLUS_2               9                13
  CLUS_3               2                13
  CLUS_4               1                 9
D9V4, multiclass
D9V5, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               5                17
  CLUS_2               6                16
  CLUS_3               2                20
D9V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2   11
  8P GAIN WILD-TYPE    7   46
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               2                 7
  CLUS_2              11                46

Clustering(10) Variable = 8q gain mutation analysis
D10V1, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               0                 5
  CLUS_2              13                34
  CLUS_3               1                13
D10V2, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2                15
  CLUS_2               6                28
  CLUS_3               6                 8
D10V3, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1                18
  CLUS_2              10                12
  CLUS_3               2                13
  CLUS_4               1                 9
D10V4, multiclass
D10V5, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               5                17
  CLUS_2               6                16
  CLUS_3               3                19
D10V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      2   12
  8Q GAIN WILD-TYPE    7   45
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2                 7
  CLUS_2              12                45

Clustering(11) Variable = 9p gain mutation analysis
D11V1, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               6                41
  CLUS_3               2                12
D11V2, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               3                14
  CLUS_2               3                31
  CLUS_3               2                12
D11V3, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               3                16
  CLUS_2               3                19
  CLUS_3               1                14
  CLUS_4               1                 9
D11V4, multiclass
D11V5, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2                20
  CLUS_2               4                18
  CLUS_3               2                20
D11V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    6
  9P GAIN WILD-TYPE    7   51
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               6                51

Clustering(12) Variable = 9q gain mutation analysis
D12V1, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               6                41
  CLUS_3               2                12
D12V2, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               3                14
  CLUS_2               3                31
  CLUS_3               2                12
D12V3, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               3                16
  CLUS_2               3                19
  CLUS_3               1                14
  CLUS_4               1                 9
D12V4, multiclass
D12V5, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2                20
  CLUS_2               4                18
  CLUS_3               2                20
D12V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2    6
  9Q GAIN WILD-TYPE    7   51
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               6                51

Clustering(13) Variable = 11p gain mutation analysis
D13V1, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                  5
  CLUS_2                9                 38
  CLUS_3                4                 10
D13V2, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                2                 15
  CLUS_2                6                 28
  CLUS_3                5                  9
D13V3, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                 18
  CLUS_2               11                 11
  CLUS_3                1                 14
  CLUS_4                0                 10
D13V4, multiclass
D13V5, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                4                 18
  CLUS_2                5                 17
  CLUS_3                4                 18
D13V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0   13
  11P GAIN WILD-TYPE    9   44
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                  9
  CLUS_2               13                 44

Clustering(14) Variable = 11q gain mutation analysis
D14V1, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                  5
  CLUS_2               10                 37
  CLUS_3                4                 10
D14V2, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                2                 15
  CLUS_2                7                 27
  CLUS_3                5                  9
D14V3, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                 18
  CLUS_2               12                 10
  CLUS_3                1                 14
  CLUS_4                0                 10
D14V4, multiclass
D14V5, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                4                 18
  CLUS_2                5                 17
  CLUS_3                5                 17
D14V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   14
  11Q GAIN WILD-TYPE    9   43
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                  9
  CLUS_2               14                 43

Clustering(15) Variable = 12p gain mutation analysis
D15V1, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                0                  5
  CLUS_2               11                 36
  CLUS_3                3                 11
D15V2, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                3                 14
  CLUS_2                6                 28
  CLUS_3                5                  9
D15V3, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                2                 17
  CLUS_2               10                 12
  CLUS_3                1                 14
  CLUS_4                1                  9
D15V4, multiclass
D15V5, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                3                 19
  CLUS_2                7                 15
  CLUS_3                4                 18
D15V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2   12
  12P GAIN WILD-TYPE    7   45
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                2                  7
  CLUS_2               12                 45

Clustering(16) Variable = 12q gain mutation analysis
D16V1, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                0                  5
  CLUS_2               10                 37
  CLUS_3                3                 11
D16V2, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                3                 14
  CLUS_2                6                 28
  CLUS_3                4                 10
D16V3, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                3                 16
  CLUS_2                9                 13
  CLUS_3                0                 15
  CLUS_4                1                  9
D16V4, multiclass
D16V5, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                 20
  CLUS_2                6                 16
  CLUS_3                5                 17
D16V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1   12
  12Q GAIN WILD-TYPE    8   45
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                  8
  CLUS_2               12                 45

Clustering(17) Variable = 14q gain mutation analysis
D17V1, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                0                  5
  CLUS_2               11                 36
  CLUS_3                5                  9
D17V2, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                4                 13
  CLUS_2                7                 27
  CLUS_3                5                  9
D17V3, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                3                 16
  CLUS_2               12                 10
  CLUS_3                1                 14
  CLUS_4                0                 10
D17V4, multiclass
D17V5, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                3                 19
  CLUS_2                7                 15
  CLUS_3                6                 16
D17V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1   15
  14Q GAIN WILD-TYPE    8   42
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                  8
  CLUS_2               15                 42

Clustering(18) Variable = 15q gain mutation analysis
D18V1, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                0                  5
  CLUS_2                9                 38
  CLUS_3                5                  9
D18V2, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                4                 13
  CLUS_2                5                 29
  CLUS_3                5                  9
D18V3, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                2                 17
  CLUS_2               11                 11
  CLUS_3                1                 14
  CLUS_4                0                 10
D18V4, multiclass
D18V5, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                4                 18
  CLUS_2                6                 16
  CLUS_3                4                 18
D18V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1   13
  15Q GAIN WILD-TYPE    8   44
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                1                  8
  CLUS_2               13                 44

Clustering(19) Variable = 16p gain mutation analysis
D19V1, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                0                  5
  CLUS_2               11                 36
  CLUS_3                4                 10
D19V2, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                3                 14
  CLUS_2                8                 26
  CLUS_3                4                 10
D19V3, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                3                 16
  CLUS_2               12                 10
  CLUS_3                0                 15
  CLUS_4                0                 10
D19V4, multiclass
D19V5, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                 20
  CLUS_2                8                 14
  CLUS_3                5                 17
D19V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0   15
  16P GAIN WILD-TYPE    9   42
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                0                  9
  CLUS_2               15                 42

Clustering(20) Variable = 16q gain mutation analysis
D20V1, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                0                  5
  CLUS_2               11                 36
  CLUS_3                4                 10
D20V2, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                3                 14
  CLUS_2                8                 26
  CLUS_3                4                 10
D20V3, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                3                 16
  CLUS_2               12                 10
  CLUS_3                0                 15
  CLUS_4                0                 10
D20V4, multiclass
D20V5, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                 20
  CLUS_2                8                 14
  CLUS_3                5                 17
D20V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   15
  16Q GAIN WILD-TYPE    9   42
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                0                  9
  CLUS_2               15                 42

Clustering(21) Variable = 18p gain mutation analysis
D21V1, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                  5
  CLUS_2               12                 35
  CLUS_3                2                 12
D21V2, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                3                 14
  CLUS_2                5                 29
  CLUS_3                5                  9
D21V3, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                 18
  CLUS_2               10                 12
  CLUS_3                1                 14
  CLUS_4                2                  8
D21V4, multiclass
D21V5, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                4                 18
  CLUS_2                5                 17
  CLUS_3                5                 17
D21V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3   11
  18P GAIN WILD-TYPE    6   46
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                3                  6
  CLUS_2               11                 46

Clustering(22) Variable = 18q gain mutation analysis
D22V1, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                  5
  CLUS_2               11                 36
  CLUS_3                2                 12
D22V2, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                3                 14
  CLUS_2                5                 29
  CLUS_3                4                 10
D22V3, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                 18
  CLUS_2               10                 12
  CLUS_3                1                 14
  CLUS_4                1                  9
D22V4, multiclass
D22V5, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                3                 19
  CLUS_2                5                 17
  CLUS_3                5                 17
D22V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2   11
  18Q GAIN WILD-TYPE    7   46
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                  7
  CLUS_2               11                 46

Clustering(23) Variable = 19p gain mutation analysis
D23V1, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                  5
  CLUS_2                9                 38
  CLUS_3                2                 12
D23V2, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                2                 15
  CLUS_2                7                 27
  CLUS_3                2                 12
D23V3, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                2                 17
  CLUS_2                9                 13
  CLUS_3                0                 15
  CLUS_4                0                 10
D23V4, multiclass
D23V5, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                2                 20
  CLUS_2                6                 16
  CLUS_3                3                 19
D23V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0   11
  19P GAIN WILD-TYPE    9   46
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                  9
  CLUS_2               11                 46

Clustering(24) Variable = 19q gain mutation analysis
D24V1, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                  5
  CLUS_2                8                 39
  CLUS_3                1                 13
D24V2, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                 15
  CLUS_2                6                 28
  CLUS_3                1                 13
D24V3, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                8                 14
  CLUS_3                0                 15
  CLUS_4                0                 10
D24V4, multiclass
D24V5, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                 21
  CLUS_2                6                 16
  CLUS_3                2                 20
D24V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0    9
  19Q GAIN WILD-TYPE    9   48
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                9                 48

Clustering(25) Variable = 20p gain mutation analysis
D25V1, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                0                  5
  CLUS_2                9                 38
  CLUS_3                5                  9
D25V2, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                4                 13
  CLUS_2                6                 28
  CLUS_3                4                 10
D25V3, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                3                 16
  CLUS_2               10                 12
  CLUS_3                0                 15
  CLUS_4                1                  9
D25V4, multiclass
D25V5, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                3                 19
  CLUS_2                7                 15
  CLUS_3                4                 18
D25V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1   13
  20P GAIN WILD-TYPE    8   44
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                1                  8
  CLUS_2               13                 44

Clustering(26) Variable = 20q gain mutation analysis
D26V1, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                0                  5
  CLUS_2               10                 37
  CLUS_3                5                  9
D26V2, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                4                 13
  CLUS_2                6                 28
  CLUS_3                5                  9
D26V3, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                3                 16
  CLUS_2               10                 12
  CLUS_3                0                 15
  CLUS_4                2                  8
D26V4, multiclass
D26V5, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                4                 18
  CLUS_2                7                 15
  CLUS_3                4                 18
D26V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      2   13
  20Q GAIN WILD-TYPE    7   44
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                2                  7
  CLUS_2               13                 44

Clustering(27) Variable = 21q gain mutation analysis
D27V1, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                  5
  CLUS_2                2                 45
  CLUS_3                1                 13
D27V2, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 63 
        TCGA-KL-8323         TCGA-KL-8324         TCGA-KL-8325 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8326         TCGA-KL-8327         TCGA-KL-8328 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8329         TCGA-KL-8330         TCGA-KL-8331 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8332         TCGA-KL-8333         TCGA-KL-8334 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8335         TCGA-KL-8336         TCGA-KL-8337 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8338         TCGA-KL-8339         TCGA-KL-8340 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8341         TCGA-KL-8342         TCGA-KL-8343 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KL-8344         TCGA-KL-8345         TCGA-KL-8346 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KM-8439         TCGA-KM-8440         TCGA-KM-8441 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KM-8442         TCGA-KM-8443         TCGA-KM-8476 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KM-8477         TCGA-KN-8418         TCGA-KN-8419 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8421         TCGA-KN-8422         TCGA-KN-8423 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8424         TCGA-KN-8425         TCGA-KN-8426 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8430         TCGA-KN-8431         TCGA-KN-8432 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8434         TCGA-KN-8435         TCGA-KN-8436 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KN-8437         TCGA-KO-8403         TCGA-KO-8404 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-KO-8414 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D27V3, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                2                 20
  CLUS_3                0                 15
  CLUS_4                1                  9
D27V4, multiclass
D27V5, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                2                 20
  CLUS_2                1                 21
  CLUS_3                0                 22
D27V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1    2
  21Q GAIN WILD-TYPE    8   55
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                2                 55

Clustering(28) Variable = 22q gain mutation analysis
D28V1, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                1                  4
  CLUS_2               10                 37
  CLUS_3                4                 10
D28V2, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                4                 13
  CLUS_2                5                 29
  CLUS_3                6                  8
D28V3, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                4                 15
  CLUS_2                9                 13
  CLUS_3                1                 14
  CLUS_4                1                  9
D28V4, multiclass
D28V5, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                4                 18
  CLUS_2                6                 16
  CLUS_3                5                 17
D28V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2   13
  22Q GAIN WILD-TYPE    7   44
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                2                  7
  CLUS_2               13                 44

Clustering(29) Variable = Xq gain mutation analysis
D29V1, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               7                40
  CLUS_3               2                12
D29V2, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                16
  CLUS_2               5                29
  CLUS_3               3                11
D29V3, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                19
  CLUS_2               9                13
  CLUS_3               0                15
  CLUS_4               0                10
D29V4, multiclass
D29V5, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                21
  CLUS_2               5                17
  CLUS_3               3                19
D29V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0    9
  XQ GAIN WILD-TYPE    9   48
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               9                48

Clustering(30) Variable = 1p loss mutation analysis
D30V1, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               5                 0
  CLUS_2              32                15
  CLUS_3              11                 3
D30V2, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              16                 1
  CLUS_2              29                 5
  CLUS_3               3                11
D30V3, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              19                 0
  CLUS_2              12                10
  CLUS_3              14                 1
  CLUS_4               3                 7
D30V4, multiclass
D30V5, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              12                10
  CLUS_2              17                 5
  CLUS_3              19                 3
D30V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2   46
  1P LOSS WILD-TYPE    7   11
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               2                 7
  CLUS_2              46                11

Clustering(31) Variable = 1q loss mutation analysis
D31V1, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               5                 0
  CLUS_2              31                16
  CLUS_3              11                 3
D31V2, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1              16                 1
  CLUS_2              28                 6
  CLUS_3               3                11
D31V3, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1              19                 0
  CLUS_2              12                10
  CLUS_3              13                 2
  CLUS_4               3                 7
D31V4, multiclass
D31V5, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1              11                11
  CLUS_2              17                 5
  CLUS_3              19                 3
D31V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2   45
  1Q LOSS WILD-TYPE    7   12
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               2                 7
  CLUS_2              45                12

Clustering(32) Variable = 2p loss mutation analysis
D32V1, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               5                 0
  CLUS_2              27                20
  CLUS_3              11                 3
D32V2, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              16                 1
  CLUS_2              25                 9
  CLUS_3               2                12
D32V3, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              19                 0
  CLUS_2              11                11
  CLUS_3              13                 2
  CLUS_4               0                10
D32V4, multiclass
D32V5, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               9                13
  CLUS_2              16                 6
  CLUS_3              18                 4
D32V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1   42
  2P LOSS WILD-TYPE    8   15
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               1                 8
  CLUS_2              42                15

Clustering(33) Variable = 2q loss mutation analysis
D33V1, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               5                 0
  CLUS_2              27                20
  CLUS_3              11                 3
D33V2, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              16                 1
  CLUS_2              25                 9
  CLUS_3               2                12
D33V3, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              19                 0
  CLUS_2              11                11
  CLUS_3              13                 2
  CLUS_4               0                10
D33V4, multiclass
D33V5, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               9                13
  CLUS_2              16                 6
  CLUS_3              18                 4
D33V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1   42
  2Q LOSS WILD-TYPE    8   15
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1                 8
  CLUS_2              42                15

Clustering(34) Variable = 3p loss mutation analysis
D34V1, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               3                44
  CLUS_3               4                10
D34V2, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               2                15
  CLUS_2               4                30
  CLUS_3               1                13
D34V3, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                19
  CLUS_2               4                18
  CLUS_3               2                13
  CLUS_4               1                 9
D34V4, multiclass
D34V5, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               2                20
  CLUS_2               1                21
  CLUS_3               4                18
D34V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0    7
  3P LOSS WILD-TYPE    9   50
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               7                50

Clustering(35) Variable = 3q loss mutation analysis
D35V1, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               2                45
  CLUS_3               4                10
D35V2, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               2                15
  CLUS_2               4                30
  CLUS_3               0                14
D35V3, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                19
  CLUS_2               4                18
  CLUS_3               2                13
  CLUS_4               0                10
D35V4, multiclass
D35V5, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                21
  CLUS_2               1                21
  CLUS_3               4                18
D35V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    6
  3Q LOSS WILD-TYPE    9   51
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               6                51

Clustering(36) Variable = 5p loss mutation analysis
D36V1, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               7                40
  CLUS_3               0                14
D36V2, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               0                17
  CLUS_2               6                28
  CLUS_3               1                13
D36V3, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               1                18
  CLUS_2               6                16
  CLUS_3               0                15
  CLUS_4               0                10
D36V4, multiclass
D36V5, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               1                21
  CLUS_2               5                17
  CLUS_3               1                21
D36V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0    7
  5P LOSS WILD-TYPE    9   50
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               7                50

Clustering(37) Variable = 5q loss mutation analysis
D37V1, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               7                40
  CLUS_3               0                14
D37V2, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                17
  CLUS_2               6                28
  CLUS_3               1                13
D37V3, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               1                18
  CLUS_2               6                16
  CLUS_3               0                15
  CLUS_4               0                10
D37V4, multiclass
D37V5, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               1                21
  CLUS_2               5                17
  CLUS_3               1                21
D37V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0    7
  5Q LOSS WILD-TYPE    9   50
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               7                50

Clustering(38) Variable = 6p loss mutation analysis
D38V1, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               5                 0
  CLUS_2              31                16
  CLUS_3              11                 3
D38V2, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              16                 1
  CLUS_2              27                 7
  CLUS_3               4                10
D38V3, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              19                 0
  CLUS_2              12                10
  CLUS_3              14                 1
  CLUS_4               2                 8
D38V4, multiclass
D38V5, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              11                11
  CLUS_2              17                 5
  CLUS_3              19                 3
D38V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2   45
  6P LOSS WILD-TYPE    7   12
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2                 7
  CLUS_2              45                12

Clustering(39) Variable = 6q loss mutation analysis
D39V1, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               5                 0
  CLUS_2              31                16
  CLUS_3              11                 3
D39V2, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              16                 1
  CLUS_2              27                 7
  CLUS_3               4                10
D39V3, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              19                 0
  CLUS_2              12                10
  CLUS_3              14                 1
  CLUS_4               2                 8
D39V4, multiclass
D39V5, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              11                11
  CLUS_2              17                 5
  CLUS_3              19                 3
D39V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      2   45
  6Q LOSS WILD-TYPE    7   12
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               2                 7
  CLUS_2              45                12

Clustering(40) Variable = 8p loss mutation analysis
D40V1, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               0                47
  CLUS_3               9                 5
D40V2, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               5                12
  CLUS_2               4                30
  CLUS_3               0                14
D40V3, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               6                13
  CLUS_2               1                21
  CLUS_3               2                13
  CLUS_4               0                10
D40V4, multiclass
D40V5, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               1                21
  CLUS_2               2                20
  CLUS_3               6                16
D40V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0    9
  8P LOSS WILD-TYPE    9   48
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               9                48

Clustering(41) Variable = 8q loss mutation analysis
D41V1, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               0                47
  CLUS_3               8                 6
D41V2, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               5                12
  CLUS_2               3                31
  CLUS_3               0                14
D41V3, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               5                14
  CLUS_2               1                21
  CLUS_3               2                13
  CLUS_4               0                10
D41V4, multiclass
D41V5, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               1                21
  CLUS_2               2                20
  CLUS_3               5                17
D41V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0    8
  8Q LOSS WILD-TYPE    9   49
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               8                49

Clustering(42) Variable = 9p loss mutation analysis
D42V1, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               6                41
  CLUS_3               2                12
D42V2, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               2                15
  CLUS_2               4                30
  CLUS_3               2                12
D42V3, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               0                19
  CLUS_2               4                18
  CLUS_3               2                13
  CLUS_4               2                 8
D42V4, multiclass
D42V5, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               2                20
  CLUS_2               4                18
  CLUS_3               2                20
D42V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2    6
  9P LOSS WILD-TYPE    7   51
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               6                51

Clustering(43) Variable = 9q loss mutation analysis
D43V1, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               6                41
  CLUS_3               2                12
D43V2, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               2                15
  CLUS_2               4                30
  CLUS_3               2                12
D43V3, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               0                19
  CLUS_2               4                18
  CLUS_3               2                13
  CLUS_4               2                 8
D43V4, multiclass
D43V5, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               2                20
  CLUS_2               4                18
  CLUS_3               2                20
D43V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2    6
  9Q LOSS WILD-TYPE    7   51
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               6                51

Clustering(44) Variable = 10p loss mutation analysis
D44V1, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                5                  0
  CLUS_2               29                 18
  CLUS_3               10                  4
D44V2, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               16                  1
  CLUS_2               23                 11
  CLUS_3                5                  9
D44V3, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               19                  0
  CLUS_2                9                 13
  CLUS_3               13                  2
  CLUS_4                3                  7
D44V4, multiclass
D44V5, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               12                 10
  CLUS_2               14                  8
  CLUS_3               18                  4
D44V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      3   41
  10P LOSS WILD-TYPE    6   16
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                3                  6
  CLUS_2               41                 16

Clustering(45) Variable = 10q loss mutation analysis
D45V1, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                5                  0
  CLUS_2               29                 18
  CLUS_3               10                  4
D45V2, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               16                  1
  CLUS_2               23                 11
  CLUS_3                5                  9
D45V3, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               19                  0
  CLUS_2                9                 13
  CLUS_3               13                  2
  CLUS_4                3                  7
D45V4, multiclass
D45V5, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               12                 10
  CLUS_2               14                  8
  CLUS_3               18                  4
D45V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3   41
  10Q LOSS WILD-TYPE    6   16
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                3                  6
  CLUS_2               41                 16

Clustering(46) Variable = 11p loss mutation analysis
D46V1, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                0                  5
  CLUS_2                4                 43
  CLUS_3                1                 13
D46V2, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                2                 15
  CLUS_2                3                 31
  CLUS_3                0                 14
D46V3, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                3                 16
  CLUS_2                0                 22
  CLUS_3                2                 13
  CLUS_4                0                 10
D46V4, multiclass
D46V5, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                 21
  CLUS_2                1                 21
  CLUS_3                3                 19
D46V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0    5
  11P LOSS WILD-TYPE    9   52
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                5                 52

Clustering(47) Variable = 11q loss mutation analysis
D47V1, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                0                  5
  CLUS_2                4                 43
  CLUS_3                1                 13
D47V2, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                 15
  CLUS_2                3                 31
  CLUS_3                0                 14
D47V3, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                3                 16
  CLUS_2                0                 22
  CLUS_3                2                 13
  CLUS_4                0                 10
D47V4, multiclass
D47V5, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                1                 21
  CLUS_2                1                 21
  CLUS_3                3                 19
D47V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0    5
  11Q LOSS WILD-TYPE    9   52
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                5                 52

Clustering(48) Variable = 13q loss mutation analysis
D48V1, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                5                  0
  CLUS_2               25                 22
  CLUS_3                7                  7
D48V2, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               10                  7
  CLUS_2               24                 10
  CLUS_3                3                 11
D48V3, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               14                  5
  CLUS_2               10                 12
  CLUS_3               12                  3
  CLUS_4                1                  9
D48V4, multiclass
D48V5, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               10                 12
  CLUS_2               13                  9
  CLUS_3               14                  8
D48V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2   35
  13Q LOSS WILD-TYPE    7   22
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                2                  7
  CLUS_2               35                 22

Clustering(49) Variable = 16p loss mutation analysis
D49V1, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                  5
  CLUS_2                3                 44
  CLUS_3                0                 14
D49V2, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                 17
  CLUS_2                3                 31
  CLUS_3                0                 14
D49V3, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                0                 22
  CLUS_3                3                 12
  CLUS_4                0                 10
D49V4, multiclass
D49V5, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                1                 21
  CLUS_2                1                 21
  CLUS_3                1                 21
D49V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0    3
  16P LOSS WILD-TYPE    9   54
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                3                 54

Clustering(50) Variable = 16q loss mutation analysis
D50V1, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                  5
  CLUS_2                4                 43
  CLUS_3                0                 14
D50V2, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 17
  CLUS_2                3                 31
  CLUS_3                1                 13
D50V3, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                0                 22
  CLUS_3                4                 11
  CLUS_4                0                 10
D50V4, multiclass
D50V5, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                2                 20
  CLUS_2                1                 21
  CLUS_3                1                 21
D50V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1    3
  16Q LOSS WILD-TYPE    8   54
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                3                 54

Clustering(51) Variable = 17p loss mutation analysis
D51V1, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                5                  0
  CLUS_2               29                 18
  CLUS_3               11                  3
D51V2, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               16                  1
  CLUS_2               27                  7
  CLUS_3                2                 12
D51V3, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               19                  0
  CLUS_2               12                 10
  CLUS_3               14                  1
  CLUS_4                0                 10
D51V4, multiclass
D51V5, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                9                 13
  CLUS_2               17                  5
  CLUS_3               19                  3
D51V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1   44
  17P LOSS WILD-TYPE    8   13
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                1                  8
  CLUS_2               44                 13

Clustering(52) Variable = 17q loss mutation analysis
D52V1, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                5                  0
  CLUS_2               29                 18
  CLUS_3               11                  3
D52V2, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               16                  1
  CLUS_2               27                  7
  CLUS_3                2                 12
D52V3, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               19                  0
  CLUS_2               12                 10
  CLUS_3               14                  1
  CLUS_4                0                 10
D52V4, multiclass
D52V5, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                9                 13
  CLUS_2               17                  5
  CLUS_3               19                  3
D52V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1   44
  17Q LOSS WILD-TYPE    8   13
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                  8
  CLUS_2               44                 13

Clustering(53) Variable = 18p loss mutation analysis
D53V1, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                1                  4
  CLUS_2                4                 43
  CLUS_3                0                 14
D53V2, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                 17
  CLUS_2                5                 29
  CLUS_3                0                 14
D53V3, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                0                 22
  CLUS_3                4                 11
  CLUS_4                0                 10
D53V4, multiclass
D53V5, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                1                 21
  CLUS_2                1                 21
  CLUS_3                3                 19
D53V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      0    5
  18P LOSS WILD-TYPE    9   52
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                5                 52

Clustering(54) Variable = 18q loss mutation analysis
D54V1, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                  4
  CLUS_2                6                 41
  CLUS_3                0                 14
D54V2, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                 17
  CLUS_2                6                 28
  CLUS_3                1                 13
D54V3, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                2                 17
  CLUS_2                0                 22
  CLUS_3                4                 11
  CLUS_4                1                  9
D54V4, multiclass
D54V5, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                2                 20
  CLUS_2                1                 21
  CLUS_3                4                 18
D54V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1    6
  18Q LOSS WILD-TYPE    8   51
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                6                 51

Clustering(55) Variable = 21q loss mutation analysis
D55V1, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                  3
  CLUS_2               20                 27
  CLUS_3                6                  8
D55V2, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               11                  6
  CLUS_2               15                 19
  CLUS_3                2                 12
D55V3, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               11                  8
  CLUS_2                8                 14
  CLUS_3                7                  8
  CLUS_4                2                  8
D55V4, multiclass
D55V5, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                8                 14
  CLUS_2                9                 13
  CLUS_3               11                 11
D55V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3   25
  21Q LOSS WILD-TYPE    6   32
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                3                  6
  CLUS_2               25                 32

Clustering(56) Variable = 22q loss mutation analysis
D56V1, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                0                  5
  CLUS_2                5                 42
  CLUS_3                0                 14
D56V2, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                0                 17
  CLUS_2                5                 29
  CLUS_3                0                 14
D56V3, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                3                 19
  CLUS_3                1                 14
  CLUS_4                0                 10
D56V4, multiclass
D56V5, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                0                 22
  CLUS_2                3                 19
  CLUS_3                2                 20
D56V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      0    5
  22Q LOSS WILD-TYPE    9   52
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                5                 52

Clustering(57) Variable = Xq loss mutation analysis
D57V1, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               3                 2
  CLUS_2              22                25
  CLUS_3               8                 6
D57V2, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              12                 5
  CLUS_2              21                13
  CLUS_3               0                14
D57V3, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              15                 4
  CLUS_2               8                14
  CLUS_3              10                 5
  CLUS_4               0                10
D57V4, multiclass
D57V5, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               6                16
  CLUS_2              13                 9
  CLUS_3              14                 8
D57V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0   33
  XQ LOSS WILD-TYPE    9   24
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                 9
  CLUS_2              33                24
                     V1                      V2                      V3 
              "CN_CNMF"      "METHLYATION_CNMF"          "MRNASEQ_CNMF" 
                     V4                      V5                      V6 
"MRNASEQ_CHIERARCHICAL"           "MIRSEQ_CNMF"  "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
