
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/399350/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/SKCM-All_Samples/3161161/1.GDAC_mergedClustering.Finished/SKCM-All_Samples.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SKCM-All_Samples", "-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_Samples"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=316, in cluster file=288, common to both=288
[1] "Reduce the number of clustering variables from 80 to 78."
[1]  78 288
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               32               256 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               32               256 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               89               199 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               89               199 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               31               257 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               31               257 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               28               260 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               28               260 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               25               263 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               25               263 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               32               256 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               32               256 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               27               261 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               27               261 
[1] "4q gain mutation analysis"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               21               267 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               21               267 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               35               253 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               35               253 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               15               273 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               15               273 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               89               199 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               89               199 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               22               266 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               22               266 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              119               169 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              119               169 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              120               168 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              120               168 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               55               233 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               55               233 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               92               196 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               92               196 
[1] "9p gain mutation analysis"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                9               279 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                9               279 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               11               277 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               11               277 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                19                269 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                19                269 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                16                272 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                16                272 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                23                265 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                23                265 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                11                277 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                11                277 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                45                243 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                45                243 
[1] "14q gain mutation analysis"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                16                272 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                16                272 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                37                251 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                37                251 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                17                271 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                17                271 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                16                272 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                16                272 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                17                271 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                17                271 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                30                258 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                30                258 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                33                255 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                33                255 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                23                265 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                23                265 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                18                270 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                18                270 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                22                266 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                22                266 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                79                209 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                79                209 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               100                188 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               100                188 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                31                257 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                31                257 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                64                224 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                64                224 
[1] "Xq gain mutation analysis"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6               282 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6               282 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               20               268 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               20               268 
[1] "1q loss mutation analysis"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                9               279 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                9               279 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               24               264 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               24               264 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               24               264 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               24               264 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               24               264 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               24               264 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               21               267 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               21               267 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               35               253 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               35               253 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               38               250 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               38               250 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               34               254 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               34               254 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               52               236 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               52               236 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               25               263 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               25               263 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              100               188 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              100               188 
[1] "7p loss mutation analysis"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                7               281 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                7               281 
[1] "7q loss mutation analysis"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6               282 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6               282 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               36               252 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               36               252 
[1] "8q loss mutation analysis"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9               279 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9               279 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              159               129 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              159               129 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              115               173 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              115               173 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               120                168 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               120                168 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               135                153 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               135                153 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                63                225 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                63                225 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                72                216 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                72                216 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                21                267 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                21                267 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                31                257 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                31                257 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                40                248 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                40                248 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                61                227 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                61                227 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                17                271 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                17                271 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                24                264 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                24                264 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                57                231 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                57                231 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                56                232 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                56                232 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                27                261 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                27                261 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                54                234 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                54                234 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                49                239 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                49                239 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                22                266 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                22                266 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                22                266 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                22                266 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                14                274 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                14                274 
[1] "20q loss mutation analysis"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                285 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                285 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                33                255 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                33                255 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                24                264 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                24                264 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                9               279 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                9               279 
[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 288 columns.

Variable 1:'CN_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=3,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=2,	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 288 columns, 0 survival variables, and 8 non-survival variables.
CN_CNMF, nv=4, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain mutation analysis
D1V1, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               5                49
  CLUS_2              13                82
  CLUS_3               4                64
  CLUS_4              10                61
D1V2, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               7                64
  CLUS_2              15                90
  CLUS_3              10               102
D1V3, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              12                61
  CLUS_2               4                38
  CLUS_3               6                41
D1V4, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               9                44
  CLUS_2               8                63
  CLUS_3               5                33
D1V5, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               3                41
  CLUS_2              11                70
  CLUS_3               9                76
  CLUS_4               8                64
D1V6, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              10                69
  CLUS_2              10               105
  CLUS_3              11                77
D1V7, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              14               108
  CLUS_2              12                76
  CLUS_3               6                66
D1V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     23    9
  1P GAIN WILD-TYPE  153   97
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              23               153
  CLUS_2               9                97

Clustering(2) Variable = 1q gain mutation analysis
D2V1, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               9                45
  CLUS_2              40                55
  CLUS_3              13                55
  CLUS_4              27                44
D2V2, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              28                43
  CLUS_2              32                73
  CLUS_3              29                83
D2V3, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              23                50
  CLUS_2              15                27
  CLUS_3              14                33
D2V4, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              15                38
  CLUS_2              24                47
  CLUS_3              13                25
D2V5, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               6                38
  CLUS_2              34                47
  CLUS_3              27                58
  CLUS_4              19                53
D2V6, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              25                54
  CLUS_2              36                79
  CLUS_3              25                63
D2V7, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              45                77
  CLUS_2              22                66
  CLUS_3              21                51
D2V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     64   24
  1Q GAIN WILD-TYPE  112   82
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              64               112
  CLUS_2              24                82

Clustering(3) Variable = 2p gain mutation analysis
D3V1, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               3                51
  CLUS_2              11                84
  CLUS_3               2                66
  CLUS_4              15                56
D3V2, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              12                59
  CLUS_2              10                95
  CLUS_3               9               103
D3V3, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               8                65
  CLUS_2               3                39
  CLUS_3               8                39
D3V4, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               7                46
  CLUS_2               6                65
  CLUS_3               6                32
D3V5, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               2                42
  CLUS_2              10                71
  CLUS_3              16                69
  CLUS_4               3                69
D3V6, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               8                71
  CLUS_2               8               107
  CLUS_3              15                73
D3V7, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              10               112
  CLUS_2              15                73
  CLUS_3               6                66
D3V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     12   19
  2P GAIN WILD-TYPE  164   87
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              12               164
  CLUS_2              19                87

Clustering(4) Variable = 2q gain mutation analysis
D4V1, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               2                52
  CLUS_2               9                86
  CLUS_3               2                66
  CLUS_4              15                56
D4V2, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               9                62
  CLUS_2              11                94
  CLUS_3               8               104
D4V3, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               7                66
  CLUS_2               2                40
  CLUS_3               8                39
D4V4, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               8                45
  CLUS_2               3                68
  CLUS_3               6                32
D4V5, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               2                42
  CLUS_2               7                74
  CLUS_3              16                69
  CLUS_4               3                69
D4V6, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               6                73
  CLUS_2               7               108
  CLUS_3              15                73
D4V7, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               7               115
  CLUS_2              15                73
  CLUS_3               6                66
D4V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      9   19
  2Q GAIN WILD-TYPE  167   87
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               9               167
  CLUS_2              19                87

Clustering(5) Variable = 3p gain mutation analysis
D5V1, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3                51
  CLUS_2               9                86
  CLUS_3               2                66
  CLUS_4              11                60
D5V2, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               8                63
  CLUS_2              11                94
  CLUS_3               6               106
D5V3, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               6                67
  CLUS_2               4                38
  CLUS_3               5                42
D5V4, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               5                48
  CLUS_2               7                64
  CLUS_3               3                35
D5V5, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               0                44
  CLUS_2               8                73
  CLUS_3              11                74
  CLUS_4               5                67
D5V6, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               7                72
  CLUS_2               6               109
  CLUS_3              11                77
D5V7, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              11               111
  CLUS_2               8                80
  CLUS_3               5                67
D5V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     15    9
  3P GAIN WILD-TYPE  161   97
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              15               161
  CLUS_2               9                97

Clustering(6) Variable = 3q gain mutation analysis
D6V1, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               6                48
  CLUS_2              11                84
  CLUS_3               3                65
  CLUS_4              12                59
D6V2, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              10                61
  CLUS_2              13                92
  CLUS_3               9               103
D6V3, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               8                65
  CLUS_2               4                38
  CLUS_3               8                39
D6V4, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               6                47
  CLUS_2               9                62
  CLUS_3               5                33
D6V5, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               1                43
  CLUS_2               8                73
  CLUS_3              15                70
  CLUS_4               7                65
D6V6, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               9                70
  CLUS_2               9               106
  CLUS_3              13                75
D6V7, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              12               110
  CLUS_2              11                77
  CLUS_3               8                64
D6V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     18   13
  3Q GAIN WILD-TYPE  158   93
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              18               158
  CLUS_2              13                93

Clustering(7) Variable = 4p gain mutation analysis
D7V1, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               3                51
  CLUS_2              14                81
  CLUS_3               1                67
  CLUS_4               9                62
D7V2, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               9                62
  CLUS_2              14                91
  CLUS_3               4               108
D7V3, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               7                66
  CLUS_2               5                37
  CLUS_3               3                44
D7V4, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               3                50
  CLUS_2              10                61
  CLUS_3               2                36
D7V5, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               2                42
  CLUS_2              10                71
  CLUS_3               9                76
  CLUS_4               5                67
D7V6, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               9                70
  CLUS_2               8               107
  CLUS_3               9                79
D7V7, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1              11               111
  CLUS_2               8                80
  CLUS_3               7                65
D7V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     17    9
  4P GAIN WILD-TYPE  159   97
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1              17               159
  CLUS_2               9                97

Clustering(8) Variable = 4q gain mutation analysis
D8V1, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2                52
  CLUS_2              10                85
  CLUS_3               1                67
  CLUS_4               8                63
D8V2, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               5                66
  CLUS_2              13                92
  CLUS_3               3               109
D8V3, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               6                67
  CLUS_2               2                40
  CLUS_3               3                44
D8V4, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               3                50
  CLUS_2               6                65
  CLUS_3               2                36
D8V5, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2                42
  CLUS_2               9                72
  CLUS_3               6                79
  CLUS_4               4                68
D8V6, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               7                72
  CLUS_2               8               107
  CLUS_3               6                82
D8V7, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1              10               112
  CLUS_2               5                83
  CLUS_3               6                66
D8V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     15    6
  4Q GAIN WILD-TYPE  161  100
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1              15               161
  CLUS_2               6               100

Clustering(9) Variable = 5p gain mutation analysis
D9V1, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               3                51
  CLUS_2              12                83
  CLUS_3               2                66
  CLUS_4              18                53
D9V2, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              11                60
  CLUS_2              16                89
  CLUS_3               8               104
D9V3, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               8                65
  CLUS_2               5                37
  CLUS_3               5                42
D9V4, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               7                46
  CLUS_2               7                64
  CLUS_3               4                34
D9V5, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               8                36
  CLUS_2              10                71
  CLUS_3              10                75
  CLUS_4               7                65
D9V6, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              12                67
  CLUS_2              12               103
  CLUS_3              11                77
D9V7, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              12               110
  CLUS_2              10                78
  CLUS_3              12                60
D9V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     20   14
  5P GAIN WILD-TYPE  156   92
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              20               156
  CLUS_2              14                92

Clustering(10) Variable = 5q gain mutation analysis
D10V1, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               0                54
  CLUS_2              10                85
  CLUS_3               0                68
  CLUS_4               5                66
D10V2, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               5                66
  CLUS_2               7                98
  CLUS_3               3               109
D10V3, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               3                70
  CLUS_2               2                40
  CLUS_3               2                45
D10V4, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                51
  CLUS_2               4                67
  CLUS_3               1                37
D10V5, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1                43
  CLUS_2               7                74
  CLUS_3               5                80
  CLUS_4               2                70
D10V6, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               3                76
  CLUS_2               5               110
  CLUS_3               7                81
D10V7, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               8               114
  CLUS_2               3                85
  CLUS_3               3                69
D10V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     11    3
  5Q GAIN WILD-TYPE  165  103
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              11               165
  CLUS_2               3               103

Clustering(11) Variable = 6p gain mutation analysis
D11V1, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              12                42
  CLUS_2              49                46
  CLUS_3              11                57
  CLUS_4              17                54
D11V2, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              34                37
  CLUS_2              39                66
  CLUS_3              16                96
D11V3, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              27                46
  CLUS_2              16                26
  CLUS_3              11                36
D11V4, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              20                33
  CLUS_2              24                47
  CLUS_3              10                28
D11V5, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              12                32
  CLUS_2              35                46
  CLUS_3              26                59
  CLUS_4              14                58
D11V6, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              31                48
  CLUS_2              34                81
  CLUS_3              22                66
D11V7, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              52                70
  CLUS_2              19                69
  CLUS_3              16                56
D11V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     69   18
  6P GAIN WILD-TYPE  107   88
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              69               107
  CLUS_2              18                88

Clustering(12) Variable = 6q gain mutation analysis
D12V1, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               4                50
  CLUS_2              12                83
  CLUS_3               3                65
  CLUS_4               3                68
D12V2, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               9                62
  CLUS_2               7                98
  CLUS_3               6               106
D12V3, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               8                65
  CLUS_2               3                39
  CLUS_3               3                44
D12V4, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               5                48
  CLUS_2               7                64
  CLUS_3               2                36
D12V5, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               2                42
  CLUS_2               5                76
  CLUS_3               9                76
  CLUS_4               4                68
D12V6, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               7                72
  CLUS_2               6               109
  CLUS_3               7                81
D12V7, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              11               111
  CLUS_2               6                82
  CLUS_3               3                69
D12V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     15    5
  6Q GAIN WILD-TYPE  161  101
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              15               161
  CLUS_2               5               101

Clustering(13) Variable = 7p gain mutation analysis
D13V1, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              18                36
  CLUS_2              40                55
  CLUS_3               9                59
  CLUS_4              52                19
D13V2, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              28                43
  CLUS_2              52                53
  CLUS_3              39                73
D13V3, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              30                43
  CLUS_2              12                30
  CLUS_3              26                21
D13V4, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              24                29
  CLUS_2              22                49
  CLUS_3              22                16
D13V5, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              13                31
  CLUS_2              31                50
  CLUS_3              50                35
  CLUS_4              23                49
D13V6, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              30                49
  CLUS_2              38                77
  CLUS_3              49                39
D13V7, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              46                76
  CLUS_2              37                51
  CLUS_3              33                39
D13V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     67   49
  7P GAIN WILD-TYPE  109   57
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              67               109
  CLUS_2              49                57

Clustering(14) Variable = 7q gain mutation analysis
D14V1, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              18                36
  CLUS_2              39                56
  CLUS_3              11                57
  CLUS_4              52                19
D14V2, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              27                44
  CLUS_2              51                54
  CLUS_3              42                70
D14V3, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              29                44
  CLUS_2              11                31
  CLUS_3              26                21
D14V4, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              22                31
  CLUS_2              22                49
  CLUS_3              22                16
D14V5, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              11                33
  CLUS_2              30                51
  CLUS_3              53                32
  CLUS_4              25                47
D14V6, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              28                51
  CLUS_2              40                75
  CLUS_3              51                37
D14V7, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              44                78
  CLUS_2              38                50
  CLUS_3              35                37
D14V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     65   52
  7Q GAIN WILD-TYPE  111   54
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              65               111
  CLUS_2              52                54

Clustering(15) Variable = 8p gain mutation analysis
D15V1, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               8                46
  CLUS_2              24                71
  CLUS_3               3                65
  CLUS_4              20                51
D15V2, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              20                51
  CLUS_2              22                83
  CLUS_3              13                99
D15V3, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              16                57
  CLUS_2               3                39
  CLUS_3              11                36
D15V4, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              11                42
  CLUS_2               9                62
  CLUS_3              10                28
D15V5, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              10                34
  CLUS_2              12                69
  CLUS_3              26                59
  CLUS_4               7                65
D15V6, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              16                63
  CLUS_2              12               103
  CLUS_3              27                61
D15V7, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              21               101
  CLUS_2              21                67
  CLUS_3              12                60
D15V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     30   24
  8P GAIN WILD-TYPE  146   82
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              30               146
  CLUS_2              24                82

Clustering(16) Variable = 8q gain mutation analysis
D16V1, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              13                41
  CLUS_2              44                51
  CLUS_3               4                64
  CLUS_4              31                40
D16V2, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              38                33
  CLUS_2              32                73
  CLUS_3              22                90
D16V3, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              22                51
  CLUS_2              10                32
  CLUS_3              17                30
D16V4, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              18                35
  CLUS_2              18                53
  CLUS_3              13                25
D16V5, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              14                30
  CLUS_2              30                51
  CLUS_3              38                47
  CLUS_4               9                63
D16V6, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              32                47
  CLUS_2              24                91
  CLUS_3              35                53
D16V7, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              38                84
  CLUS_2              32                56
  CLUS_3              20                52
D16V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     55   35
  8Q GAIN WILD-TYPE  121   71
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              55               121
  CLUS_2              35                71

Clustering(17) Variable = 9p gain mutation analysis
D17V1, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               1                53
  CLUS_2               4                91
  CLUS_3               1                67
  CLUS_4               3                68
D17V2, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               4                67
  CLUS_2               4               101
  CLUS_3               1               111
D17V3, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               5                68
  CLUS_2               1                41
  CLUS_3               0                47
D17V4, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2                51
  CLUS_2               4                67
  CLUS_3               0                38
D17V5, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               0                44
  CLUS_2               5                76
  CLUS_3               2                83
  CLUS_4               1                71
D17V6, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               1                78
  CLUS_2               5               110
  CLUS_3               2                86
D17V7, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               3               119
  CLUS_2               3                85
  CLUS_3               3                69
D17V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      5    4
  9P GAIN WILD-TYPE  171  102
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               5               171
  CLUS_2               4               102

Clustering(18) Variable = 9q gain mutation analysis
D18V1, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2                52
  CLUS_2               6                89
  CLUS_3               0                68
  CLUS_4               3                68
D18V2, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               4                67
  CLUS_2               5               100
  CLUS_3               2               110
D18V3, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               5                68
  CLUS_2               1                41
  CLUS_3               0                47
D18V4, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               3                50
  CLUS_2               3                68
  CLUS_3               0                38
D18V5, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1                43
  CLUS_2               5                76
  CLUS_3               3                82
  CLUS_4               2                70
D18V6, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               3                76
  CLUS_2               5               110
  CLUS_3               3                85
D18V7, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               4               118
  CLUS_2               3                85
  CLUS_3               3                69
D18V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      5    5
  9Q GAIN WILD-TYPE  171  101
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               5               171
  CLUS_2               5               101

Clustering(19) Variable = 11p gain mutation analysis
D19V1, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                 54
  CLUS_2               13                 82
  CLUS_3                3                 65
  CLUS_4                3                 68
D19V2, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                5                 66
  CLUS_2                7                 98
  CLUS_3                7                105
D19V3, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                6                 67
  CLUS_2                0                 42
  CLUS_3                4                 43
D19V4, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                7                 46
  CLUS_2                1                 70
  CLUS_3                2                 36
D19V5, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                 43
  CLUS_2                4                 77
  CLUS_3               12                 73
  CLUS_4                2                 70
D19V6, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                2                 77
  CLUS_2                5                110
  CLUS_3               12                 76
D19V7, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                6                116
  CLUS_2                7                 81
  CLUS_3                5                 67
D19V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      7   11
  11P GAIN WILD-TYPE  169   95
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                7                169
  CLUS_2               11                 95

Clustering(20) Variable = 11q gain mutation analysis
D20V1, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                 53
  CLUS_2               12                 83
  CLUS_3                0                 68
  CLUS_4                3                 68
D20V2, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                6                 65
  CLUS_2                5                100
  CLUS_3                5                107
D20V3, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                5                 68
  CLUS_2                0                 42
  CLUS_3                2                 45
D20V4, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                5                 48
  CLUS_2                1                 70
  CLUS_3                1                 37
D20V5, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                 43
  CLUS_2                2                 79
  CLUS_3               11                 74
  CLUS_4                2                 70
D20V6, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                2                 77
  CLUS_2                4                111
  CLUS_3               10                 78
D20V7, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                5                117
  CLUS_2                5                 83
  CLUS_3                5                 67
D20V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      6    9
  11Q GAIN WILD-TYPE  170   97
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                6                170
  CLUS_2                9                 97

Clustering(21) Variable = 12p gain mutation analysis
D21V1, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                3                 51
  CLUS_2                7                 88
  CLUS_3                0                 68
  CLUS_4               13                 58
D21V2, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                8                 63
  CLUS_2                9                 96
  CLUS_3                6                106
D21V3, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                8                 65
  CLUS_2                2                 40
  CLUS_3                3                 44
D21V4, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                2                 51
  CLUS_2                8                 63
  CLUS_3                3                 35
D21V5, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                 43
  CLUS_2                6                 75
  CLUS_3               15                 70
  CLUS_4                1                 71
D21V6, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                5                 74
  CLUS_2                5                110
  CLUS_3               13                 75
D21V7, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                7                115
  CLUS_2                8                 80
  CLUS_3                8                 64
D21V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      9   14
  12P GAIN WILD-TYPE  167   92
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                9                167
  CLUS_2               14                 92

Clustering(22) Variable = 12q gain mutation analysis
D22V1, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                 52
  CLUS_2                3                 92
  CLUS_3                0                 68
  CLUS_4                6                 65
D22V2, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                3                 68
  CLUS_2                4                101
  CLUS_3                4                108
D22V3, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                3                 70
  CLUS_2                1                 41
  CLUS_3                2                 45
D22V4, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                 52
  CLUS_2                3                 68
  CLUS_3                2                 36
D22V5, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                0                 44
  CLUS_2                5                 76
  CLUS_3                6                 79
  CLUS_4                0                 72
D22V6, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                 77
  CLUS_2                3                112
  CLUS_3                6                 82
D22V7, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                3                119
  CLUS_2                4                 84
  CLUS_3                4                 68
D22V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3    8
  12Q GAIN WILD-TYPE  173   98
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                3                173
  CLUS_2                8                 98

Clustering(23) Variable = 13q gain mutation analysis
D23V1, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                6                 48
  CLUS_2               33                 62
  CLUS_3                0                 68
  CLUS_4                6                 65
D23V2, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               22                 49
  CLUS_2               17                 88
  CLUS_3                6                106
D23V3, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               13                 60
  CLUS_2                4                 38
  CLUS_3                5                 42
D23V4, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                8                 45
  CLUS_2               10                 61
  CLUS_3                4                 34
D23V5, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                4                 40
  CLUS_2               12                 69
  CLUS_3               24                 61
  CLUS_4                5                 67
D23V6, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               14                 65
  CLUS_2               13                102
  CLUS_3               18                 70
D23V7, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               23                 99
  CLUS_2               13                 75
  CLUS_3                8                 64
D23V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     29   15
  13Q GAIN WILD-TYPE  147   91
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               29                147
  CLUS_2               15                 91

Clustering(24) Variable = 14q gain mutation analysis
D24V1, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                4                 50
  CLUS_2                4                 91
  CLUS_3                0                 68
  CLUS_4                8                 63
D24V2, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                6                 65
  CLUS_2                8                 97
  CLUS_3                2                110
D24V3, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                5                 68
  CLUS_2                3                 39
  CLUS_3                0                 47
D24V4, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                2                 51
  CLUS_2                5                 66
  CLUS_3                1                 37
D24V5, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                0                 44
  CLUS_2                7                 74
  CLUS_3                6                 79
  CLUS_4                3                 69
D24V6, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                4                 75
  CLUS_2                7                108
  CLUS_3                5                 83
D24V7, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                6                116
  CLUS_2                6                 82
  CLUS_3                4                 68
D24V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     10    6
  14Q GAIN WILD-TYPE  166  100
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               10                166
  CLUS_2                6                100

Clustering(25) Variable = 15q gain mutation analysis
D25V1, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                4                 50
  CLUS_2               12                 83
  CLUS_3                4                 64
  CLUS_4               17                 54
D25V2, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1               11                 60
  CLUS_2               15                 90
  CLUS_3               11                101
D25V3, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                8                 65
  CLUS_2                4                 38
  CLUS_3                4                 43
D25V4, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                6                 47
  CLUS_2                8                 63
  CLUS_3                2                 36
D25V5, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                0                 44
  CLUS_2               12                 69
  CLUS_3               16                 69
  CLUS_4                9                 63
D25V6, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                8                 71
  CLUS_2               14                101
  CLUS_3               15                 73
D25V7, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1               14                108
  CLUS_2               10                 78
  CLUS_3               10                 62
D25V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     17   17
  15Q GAIN WILD-TYPE  159   89
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1               17                159
  CLUS_2               17                 89

Clustering(26) Variable = 16p gain mutation analysis
D26V1, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                 52
  CLUS_2                9                 86
  CLUS_3                0                 68
  CLUS_4                6                 65
D26V2, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                9                 62
  CLUS_2                5                100
  CLUS_3                3                109
D26V3, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                4                 69
  CLUS_2                1                 41
  CLUS_3                4                 43
D26V4, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                3                 50
  CLUS_2                3                 68
  CLUS_3                3                 35
D26V5, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                 43
  CLUS_2                4                 77
  CLUS_3               11                 74
  CLUS_4                1                 71
D26V6, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                6                 73
  CLUS_2                3                112
  CLUS_3                8                 80
D26V7, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                4                118
  CLUS_2                9                 79
  CLUS_3                4                 68
D26V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      9    8
  16P GAIN WILD-TYPE  167   98
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                9                167
  CLUS_2                8                 98

Clustering(27) Variable = 16q gain mutation analysis
D27V1, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                 52
  CLUS_2               10                 85
  CLUS_3                0                 68
  CLUS_4                4                 67
D27V2, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                8                 63
  CLUS_2                4                101
  CLUS_3                4                108
D27V3, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                 71
  CLUS_2                2                 40
  CLUS_3                5                 42
D27V4, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                3                 50
  CLUS_2                2                 69
  CLUS_3                4                 34
D27V5, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                 43
  CLUS_2                4                 77
  CLUS_3               10                 75
  CLUS_4                1                 71
D27V6, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                6                 73
  CLUS_2                3                112
  CLUS_3                7                 81
D27V7, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                4                118
  CLUS_2                7                 81
  CLUS_3                5                 67
D27V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      7    9
  16Q GAIN WILD-TYPE  169   97
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                7                169
  CLUS_2                9                 97

Clustering(28) Variable = 17p gain mutation analysis
D28V1, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                2                 52
  CLUS_2                7                 88
  CLUS_3                1                 67
  CLUS_4                7                 64
D28V2, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                7                 64
  CLUS_2                6                 99
  CLUS_3                4                108
D28V3, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                8                 65
  CLUS_2                3                 39
  CLUS_3                2                 45
D28V4, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                5                 48
  CLUS_2                7                 64
  CLUS_3                1                 37
D28V5, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                0                 44
  CLUS_2                4                 77
  CLUS_3                8                 77
  CLUS_4                5                 67
D28V6, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                4                 75
  CLUS_2                6                109
  CLUS_3                7                 81
D28V7, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                5                117
  CLUS_2                4                 84
  CLUS_3                8                 64
D28V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      9    8
  17P GAIN WILD-TYPE  167   98
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                9                167
  CLUS_2                8                 98

Clustering(29) Variable = 17q gain mutation analysis
D29V1, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                3                 51
  CLUS_2               15                 80
  CLUS_3                2                 66
  CLUS_4               10                 61
D29V2, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               10                 61
  CLUS_2               14                 91
  CLUS_3                6                106
D29V3, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               12                 61
  CLUS_2                9                 33
  CLUS_3                2                 45
D29V4, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                6                 47
  CLUS_2               16                 55
  CLUS_3                1                 37
D29V5, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                 43
  CLUS_2               13                 68
  CLUS_3                8                 77
  CLUS_4                8                 64
D29V6, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                8                 71
  CLUS_2               15                100
  CLUS_3                7                 81
D29V7, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               15                107
  CLUS_2                5                 83
  CLUS_3                9                 63
D29V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     21    8
  17Q GAIN WILD-TYPE  155   98
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               21                155
  CLUS_2                8                 98

Clustering(30) Variable = 18p gain mutation analysis
D30V1, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                5                 49
  CLUS_2               15                 80
  CLUS_3                3                 65
  CLUS_4               10                 61
D30V2, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               10                 61
  CLUS_2               15                 90
  CLUS_3                8                104
D30V3, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               12                 61
  CLUS_2                4                 38
  CLUS_3                6                 41
D30V4, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                6                 47
  CLUS_2               12                 59
  CLUS_3                4                 34
D30V5, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                4                 40
  CLUS_2               14                 67
  CLUS_3                9                 76
  CLUS_4                6                 66
D30V6, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               12                 67
  CLUS_2               11                104
  CLUS_3               10                 78
D30V7, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               14                108
  CLUS_2                9                 79
  CLUS_3                9                 63
D30V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     19   13
  18P GAIN WILD-TYPE  157   93
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               19                157
  CLUS_2               13                 93

Clustering(31) Variable = 18q gain mutation analysis
D31V1, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                3                 51
  CLUS_2               11                 84
  CLUS_3                2                 66
  CLUS_4                7                 64
D31V2, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                7                 64
  CLUS_2               12                 93
  CLUS_3                4                108
D31V3, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                6                 67
  CLUS_2                3                 39
  CLUS_3                4                 43
D31V4, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                5                 48
  CLUS_2                5                 66
  CLUS_3                3                 35
D31V5, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                4                 40
  CLUS_2                8                 73
  CLUS_3                8                 77
  CLUS_4                2                 70
D31V6, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               10                 69
  CLUS_2                4                111
  CLUS_3                8                 80
D31V7, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               12                110
  CLUS_2                7                 81
  CLUS_3                3                 69
D31V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     16    6
  18Q GAIN WILD-TYPE  160  100
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               16                160
  CLUS_2                6                100

Clustering(32) Variable = 19p gain mutation analysis
D32V1, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                2                 52
  CLUS_2               10                 85
  CLUS_3                1                 67
  CLUS_4                5                 66
D32V2, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                8                 63
  CLUS_2                7                 98
  CLUS_3                3                109
D32V3, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                9                 64
  CLUS_2                3                 39
  CLUS_3                1                 46
D32V4, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                7                 46
  CLUS_2                5                 66
  CLUS_3                1                 37
D32V5, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                 44
  CLUS_2                7                 74
  CLUS_3               10                 75
  CLUS_4                1                 71
D32V6, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                6                 73
  CLUS_2                1                114
  CLUS_3               11                 77
D32V7, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               10                112
  CLUS_2                4                 84
  CLUS_3                4                 68
D32V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     12    6
  19P GAIN WILD-TYPE  164  100
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               12                164
  CLUS_2                6                100

Clustering(33) Variable = 19q gain mutation analysis
D33V1, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                 53
  CLUS_2               13                 82
  CLUS_3                1                 67
  CLUS_4                7                 64
D33V2, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               11                 60
  CLUS_2                6                 99
  CLUS_3                5                107
D33V3, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                9                 64
  CLUS_2                2                 40
  CLUS_3                3                 44
D33V4, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                6                 47
  CLUS_2                6                 65
  CLUS_3                2                 36
D33V5, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                 43
  CLUS_2                6                 75
  CLUS_3               14                 71
  CLUS_4                0                 72
D33V6, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                6                 73
  CLUS_2                2                113
  CLUS_3               13                 75
D33V7, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               10                112
  CLUS_2                6                 82
  CLUS_3                6                 66
D33V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     15    7
  19Q GAIN WILD-TYPE  161   99
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               15                161
  CLUS_2                7                 99

Clustering(34) Variable = 20p gain mutation analysis
D34V1, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                9                 45
  CLUS_2               35                 60
  CLUS_3                7                 61
  CLUS_4               28                 43
D34V2, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               29                 42
  CLUS_2               29                 76
  CLUS_3               21                 91
D34V3, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               24                 49
  CLUS_2                9                 33
  CLUS_3               12                 35
D34V4, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               16                 37
  CLUS_2               20                 51
  CLUS_3                9                 29
D34V5, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                6                 38
  CLUS_2               22                 59
  CLUS_3               39                 46
  CLUS_4               12                 60
D34V6, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               20                 59
  CLUS_2               23                 92
  CLUS_3               36                 52
D34V7, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               25                 97
  CLUS_2               26                 62
  CLUS_3               26                 46
D34V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     40   37
  20P GAIN WILD-TYPE  136   69
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               40                136
  CLUS_2               37                 69

Clustering(35) Variable = 20q gain mutation analysis
D35V1, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               14                 40
  CLUS_2               40                 55
  CLUS_3                8                 60
  CLUS_4               38                 33
D35V2, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               33                 38
  CLUS_2               39                 66
  CLUS_3               28                 84
D35V3, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               31                 42
  CLUS_2               14                 28
  CLUS_3               13                 34
D35V4, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               21                 32
  CLUS_2               27                 44
  CLUS_3               10                 28
D35V5, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                9                 35
  CLUS_2               28                 53
  CLUS_3               44                 41
  CLUS_4               19                 53
D35V6, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               25                 54
  CLUS_2               33                 82
  CLUS_3               42                 46
D35V7, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               38                 84
  CLUS_2               29                 59
  CLUS_3               30                 42
D35V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     54   43
  20Q GAIN WILD-TYPE  122   63
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               54                122
  CLUS_2               43                 63

Clustering(36) Variable = 21q gain mutation analysis
D36V1, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 53
  CLUS_2               17                 78
  CLUS_3                3                 65
  CLUS_4               10                 61
D36V2, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               16                 55
  CLUS_2               11                 94
  CLUS_3                4                108
D36V3, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                5                 68
  CLUS_2                2                 40
  CLUS_3                4                 43
D36V4, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                5                 48
  CLUS_2                4                 67
  CLUS_3                2                 36
D36V5, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 43
  CLUS_2                9                 72
  CLUS_3               17                 68
  CLUS_4                4                 68
D36V6, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                7                 72
  CLUS_2                8                107
  CLUS_3               16                 72
D36V7, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               11                111
  CLUS_2               14                 74
  CLUS_3                5                 67
D36V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     17   13
  21Q GAIN WILD-TYPE  159   93
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               17                159
  CLUS_2               13                 93

Clustering(37) Variable = 22q gain mutation analysis
D37V1, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                6                 48
  CLUS_2               16                 79
  CLUS_3               10                 58
  CLUS_4               32                 39
D37V2, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1               17                 54
  CLUS_2               26                 79
  CLUS_3               21                 91
D37V3, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1               17                 56
  CLUS_2                8                 34
  CLUS_3                9                 38
D37V4, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1               10                 43
  CLUS_2               17                 54
  CLUS_3                7                 31
D37V5, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                5                 39
  CLUS_2               19                 62
  CLUS_3               24                 61
  CLUS_4               14                 58
D37V6, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1               16                 63
  CLUS_2               23                 92
  CLUS_3               23                 65
D37V7, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1               24                 98
  CLUS_2               19                 69
  CLUS_3               19                 53
D37V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     36   26
  22Q GAIN WILD-TYPE  140   80
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1               36                140
  CLUS_2               26                 80

Clustering(38) Variable = Xq gain mutation analysis
D38V1, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                53
  CLUS_2               2                93
  CLUS_3               1                67
  CLUS_4               2                69
D38V2, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               3                68
  CLUS_2               2               103
  CLUS_3               1               111
D38V3, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                72
  CLUS_2               2                40
  CLUS_3               1                46
D38V4, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                53
  CLUS_2               3                68
  CLUS_3               1                37
D38V5, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                43
  CLUS_2               4                77
  CLUS_3               0                85
  CLUS_4               1                71
D38V6, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               5                74
  CLUS_2               1               114
  CLUS_3               0                88
D38V7, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               5               117
  CLUS_2               1                87
  CLUS_3               0                72
D38V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      6    0
  XQ GAIN WILD-TYPE  170  106
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               6               170
  CLUS_2               0               106

Clustering(39) Variable = 1p loss mutation analysis
D39V1, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               8                46
  CLUS_2               5                90
  CLUS_3               1                67
  CLUS_4               6                65
D39V2, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              13                58
  CLUS_2               5               100
  CLUS_3               2               110
D39V3, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               7                66
  CLUS_2               4                38
  CLUS_3               2                45
D39V4, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               3                50
  CLUS_2               8                63
  CLUS_3               2                36
D39V5, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               6                38
  CLUS_2               5                76
  CLUS_3               9                76
  CLUS_4               0                72
D39V6, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               7                72
  CLUS_2               4               111
  CLUS_3               9                79
D39V7, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              10               112
  CLUS_2               7                81
  CLUS_3               3                69
D39V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     14    6
  1P LOSS WILD-TYPE  162  100
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              14               162
  CLUS_2               6               100

Clustering(40) Variable = 1q loss mutation analysis
D40V1, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               4                50
  CLUS_2               0                95
  CLUS_3               1                67
  CLUS_4               4                67
D40V2, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               4                67
  CLUS_2               4               101
  CLUS_3               1               111
D40V3, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               0                73
  CLUS_2               2                40
  CLUS_3               2                45
D40V4, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               2                51
  CLUS_2               1                70
  CLUS_3               1                37
D40V5, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               4                40
  CLUS_2               1                80
  CLUS_3               3                82
  CLUS_4               1                71
D40V6, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               3                76
  CLUS_2               2               113
  CLUS_3               4                84
D40V7, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               4               118
  CLUS_2               3                85
  CLUS_3               2                70
D40V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      6    3
  1Q LOSS WILD-TYPE  170  103
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               6               170
  CLUS_2               3               103

Clustering(41) Variable = 2p loss mutation analysis
D41V1, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              11                43
  CLUS_2               9                86
  CLUS_3               0                68
  CLUS_4               4                67
D41V2, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              10                61
  CLUS_2               8                97
  CLUS_3               6               106
D41V3, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               9                64
  CLUS_2               6                36
  CLUS_3               1                46
D41V4, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               2                51
  CLUS_2              13                58
  CLUS_3               1                37
D41V5, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               4                40
  CLUS_2              12                69
  CLUS_3               5                80
  CLUS_4               3                69
D41V6, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              10                69
  CLUS_2               8               107
  CLUS_3               6                82
D41V7, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              21               101
  CLUS_2               1                87
  CLUS_3               2                70
D41V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     22    2
  2P LOSS WILD-TYPE  154  104
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              22               154
  CLUS_2               2               104

Clustering(42) Variable = 2q loss mutation analysis
D42V1, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               9                45
  CLUS_2              12                83
  CLUS_3               1                67
  CLUS_4               2                69
D42V2, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              11                60
  CLUS_2               9                96
  CLUS_3               4               108
D42V3, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               9                64
  CLUS_2               6                36
  CLUS_3               1                46
D42V4, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               4                49
  CLUS_2              12                59
  CLUS_3               0                38
D42V5, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               3                41
  CLUS_2              14                67
  CLUS_3               5                80
  CLUS_4               2                70
D42V6, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              10                69
  CLUS_2               8               107
  CLUS_3               6                82
D42V7, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              20               102
  CLUS_2               1                87
  CLUS_3               3                69
D42V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     21    3
  2Q LOSS WILD-TYPE  155  103
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              21               155
  CLUS_2               3               103

Clustering(43) Variable = 3p loss mutation analysis
D43V1, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               6                48
  CLUS_2               9                86
  CLUS_3               2                66
  CLUS_4               7                64
D43V2, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               7                64
  CLUS_2              12                93
  CLUS_3               5               107
D43V3, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               7                66
  CLUS_2               7                35
  CLUS_3               1                46
D43V4, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               7                46
  CLUS_2               7                64
  CLUS_3               1                37
D43V5, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1                43
  CLUS_2               5                76
  CLUS_3              15                70
  CLUS_4               3                69
D43V6, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               4                75
  CLUS_2               4               111
  CLUS_3              16                72
D43V7, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              10               112
  CLUS_2               8                80
  CLUS_3               6                66
D43V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     13   11
  3P LOSS WILD-TYPE  163   95
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              13               163
  CLUS_2              11                95

Clustering(44) Variable = 3q loss mutation analysis
D44V1, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               6                48
  CLUS_2               5                90
  CLUS_3               2                66
  CLUS_4               8                63
D44V2, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               5                66
  CLUS_2              12                93
  CLUS_3               4               108
D44V3, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               7                66
  CLUS_2               7                35
  CLUS_3               1                46
D44V4, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               5                48
  CLUS_2               9                62
  CLUS_3               1                37
D44V5, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                43
  CLUS_2               6                75
  CLUS_3              11                74
  CLUS_4               3                69
D44V6, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               5                74
  CLUS_2               5               110
  CLUS_3              11                77
D44V7, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              11               111
  CLUS_2               6                82
  CLUS_3               4                68
D44V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     13    8
  3Q LOSS WILD-TYPE  163   98
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              13               163
  CLUS_2               8                98

Clustering(45) Variable = 4p loss mutation analysis
D45V1, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               9                45
  CLUS_2              11                84
  CLUS_3               3                65
  CLUS_4              12                59
D45V2, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              13                58
  CLUS_2              13                92
  CLUS_3               9               103
D45V3, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              10                63
  CLUS_2               5                37
  CLUS_3               8                39
D45V4, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              11                42
  CLUS_2               8                63
  CLUS_3               4                34
D45V5, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               5                39
  CLUS_2              12                69
  CLUS_3              15                70
  CLUS_4               3                69
D45V6, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              11                68
  CLUS_2               9               106
  CLUS_3              15                73
D45V7, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              13               109
  CLUS_2              11                77
  CLUS_3              11                61
D45V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     20   15
  4P LOSS WILD-TYPE  156   91
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              20               156
  CLUS_2              15                91

Clustering(46) Variable = 4q loss mutation analysis
D46V1, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              10                44
  CLUS_2              13                82
  CLUS_3               1                67
  CLUS_4              14                57
D46V2, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              17                54
  CLUS_2              11                94
  CLUS_3              10               102
D46V3, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              10                63
  CLUS_2               5                37
  CLUS_3               7                40
D46V4, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              11                42
  CLUS_2               8                63
  CLUS_3               3                35
D46V5, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               5                39
  CLUS_2              12                69
  CLUS_3              17                68
  CLUS_4               4                68
D46V6, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              11                68
  CLUS_2              10               105
  CLUS_3              17                71
D46V7, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              13               109
  CLUS_2              11                77
  CLUS_3              13                59
D46V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     20   17
  4Q LOSS WILD-TYPE  156   89
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              20               156
  CLUS_2              17                89

Clustering(47) Variable = 5p loss mutation analysis
D47V1, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               9                45
  CLUS_2              10                85
  CLUS_3               2                66
  CLUS_4              13                58
D47V2, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               5                66
  CLUS_2              18                87
  CLUS_3              11               101
D47V3, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               8                65
  CLUS_2              11                31
  CLUS_3               4                43
D47V4, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               5                48
  CLUS_2              15                56
  CLUS_3               3                35
D47V5, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               3                41
  CLUS_2              14                67
  CLUS_3              10                75
  CLUS_4               7                65
D47V6, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              14                65
  CLUS_2              11               104
  CLUS_3               9                79
D47V7, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              17               105
  CLUS_2               8                80
  CLUS_3               8                64
D47V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     23   10
  5P LOSS WILD-TYPE  153   96
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              23               153
  CLUS_2              10                96

Clustering(48) Variable = 5q loss mutation analysis
D48V1, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              18                36
  CLUS_2              11                84
  CLUS_3               3                65
  CLUS_4              20                51
D48V2, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               5                66
  CLUS_2              27                78
  CLUS_3              20                92
D48V3, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              12                61
  CLUS_2              13                29
  CLUS_3               6                41
D48V4, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               9                44
  CLUS_2              17                54
  CLUS_3               5                33
D48V5, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               7                37
  CLUS_2              17                64
  CLUS_3              18                67
  CLUS_4              10                62
D48V6, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              16                63
  CLUS_2              18                97
  CLUS_3              18                70
D48V7, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              23                99
  CLUS_2              18                70
  CLUS_3              11                61
D48V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     33   19
  5Q LOSS WILD-TYPE  143   87
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              33               143
  CLUS_2              19                87

Clustering(49) Variable = 6p loss mutation analysis
D49V1, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1                53
  CLUS_2               8                87
  CLUS_3               4                64
  CLUS_4              12                59
D49V2, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               8                63
  CLUS_2               9                96
  CLUS_3               8               104
D49V3, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               7                66
  CLUS_2               2                40
  CLUS_3               7                40
D49V4, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               5                48
  CLUS_2               6                65
  CLUS_3               5                33
D49V5, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1                43
  CLUS_2               7                74
  CLUS_3              12                73
  CLUS_4               5                67
D49V6, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               4                75
  CLUS_2               8               107
  CLUS_3              13                75
D49V7, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               8               114
  CLUS_2              12                76
  CLUS_3               5                67
D49V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     12   13
  6P LOSS WILD-TYPE  164   93
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              12               164
  CLUS_2              13                93

Clustering(50) Variable = 6q loss mutation analysis
D50V1, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               3                51
  CLUS_2              46                49
  CLUS_3              11                57
  CLUS_4              40                31
D50V2, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              28                43
  CLUS_2              43                62
  CLUS_3              29                83
D50V3, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              26                47
  CLUS_2              13                29
  CLUS_3              15                32
D50V4, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              22                31
  CLUS_2              19                52
  CLUS_3              13                25
D50V5, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              13                31
  CLUS_2              26                55
  CLUS_3              42                43
  CLUS_4              18                54
D50V6, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              26                53
  CLUS_2              32                83
  CLUS_3              41                47
D50V7, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              38                84
  CLUS_2              32                56
  CLUS_3              29                43
D50V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     56   43
  6Q LOSS WILD-TYPE  120   63
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              56               120
  CLUS_2              43                63

Clustering(51) Variable = 7p loss mutation analysis
D51V1, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0                54
  CLUS_2               3                92
  CLUS_3               3                65
  CLUS_4               1                70
D51V2, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               4                67
  CLUS_2               3               102
  CLUS_3               0               112
D51V3, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               4                69
  CLUS_2               1                41
  CLUS_3               0                47
D51V4, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               1                52
  CLUS_2               4                67
  CLUS_3               0                38
D51V5, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0                44
  CLUS_2               4                77
  CLUS_3               3                82
  CLUS_4               0                72
D51V6, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               1                78
  CLUS_2               3               112
  CLUS_3               3                85
D51V7, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               4               118
  CLUS_2               1                87
  CLUS_3               2                70
D51V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      5    2
  7P LOSS WILD-TYPE  171  104
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               5               171
  CLUS_2               2               104

Clustering(52) Variable = 7q loss mutation analysis
D52V1, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               0                54
  CLUS_2               3                92
  CLUS_3               2                66
  CLUS_4               1                70
D52V2, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               4                67
  CLUS_2               1               104
  CLUS_3               1               111
D52V3, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               3                70
  CLUS_2               0                42
  CLUS_3               0                47
D52V4, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               0                53
  CLUS_2               3                68
  CLUS_3               0                38
D52V5, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               0                44
  CLUS_2               3                78
  CLUS_3               2                83
  CLUS_4               1                71
D52V6, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               1                78
  CLUS_2               3               112
  CLUS_3               2                86
D52V7, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               3               119
  CLUS_2               2                86
  CLUS_3               1                71
D52V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      4    2
  7Q LOSS WILD-TYPE  172  104
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               4               172
  CLUS_2               2               104

Clustering(53) Variable = 8p loss mutation analysis
D53V1, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               6                48
  CLUS_2              14                81
  CLUS_3               5                63
  CLUS_4              11                60
D53V2, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              10                61
  CLUS_2              17                88
  CLUS_3               9               103
D53V3, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              11                62
  CLUS_2               5                37
  CLUS_3               4                43
D53V4, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               7                46
  CLUS_2               8                63
  CLUS_3               5                33
D53V5, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               5                39
  CLUS_2              13                68
  CLUS_3              12                73
  CLUS_4               5                67
D53V6, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              13                66
  CLUS_2              12               103
  CLUS_3              10                78
D53V7, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              21               101
  CLUS_2               8                80
  CLUS_3               6                66
D53V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     28    7
  8P LOSS WILD-TYPE  148   99
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              28               148
  CLUS_2               7                99

Clustering(54) Variable = 8q loss mutation analysis
D54V1, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               4                50
  CLUS_2               1                94
  CLUS_3               2                66
  CLUS_4               2                69
D54V2, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               3                68
  CLUS_2               5               100
  CLUS_3               1               111
D54V3, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               4                69
  CLUS_2               1                41
  CLUS_3               1                46
D54V4, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               2                51
  CLUS_2               3                68
  CLUS_3               1                37
D54V5, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               2                42
  CLUS_2               3                78
  CLUS_3               4                81
  CLUS_4               0                72
D54V6, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               5                74
  CLUS_2               0               115
  CLUS_3               4                84
D54V7, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               5               117
  CLUS_2               1                87
  CLUS_3               3                69
D54V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      7    2
  8Q LOSS WILD-TYPE  169  104
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               7               169
  CLUS_2               2               104

Clustering(55) Variable = 9p loss mutation analysis
D55V1, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              38                16
  CLUS_2              71                24
  CLUS_3              13                55
  CLUS_4              37                34
D55V2, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              51                20
  CLUS_2              68                37
  CLUS_3              40                72
D55V3, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              31                42
  CLUS_2              29                13
  CLUS_3              24                23
D55V4, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              28                25
  CLUS_2              37                34
  CLUS_3              19                19
D55V5, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              25                19
  CLUS_2              48                33
  CLUS_3              60                25
  CLUS_4              26                46
D55V6, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              54                25
  CLUS_2              47                68
  CLUS_3              58                30
D55V7, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              72                50
  CLUS_2              45                43
  CLUS_3              38                34
D55V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    102   53
  9P LOSS WILD-TYPE   74   53
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1             102                74
  CLUS_2              53                53

Clustering(56) Variable = 9q loss mutation analysis
D56V1, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              26                28
  CLUS_2              46                49
  CLUS_3              12                56
  CLUS_4              31                40
D56V2, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              30                41
  CLUS_2              54                51
  CLUS_3              31                81
D56V3, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              26                47
  CLUS_2              20                22
  CLUS_3              16                31
D56V4, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              21                32
  CLUS_2              29                42
  CLUS_3              12                26
D56V5, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              17                27
  CLUS_2              30                51
  CLUS_3              43                42
  CLUS_4              25                47
D56V6, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              31                48
  CLUS_2              40                75
  CLUS_3              44                44
D56V7, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              49                73
  CLUS_2              31                57
  CLUS_3              32                40
D56V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     74   38
  9Q LOSS WILD-TYPE  102   68
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              74               102
  CLUS_2              38                68

Clustering(57) Variable = 10p loss mutation analysis
D57V1, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               32                 22
  CLUS_2               42                 53
  CLUS_3                4                 64
  CLUS_4               42                 29
D57V2, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               41                 30
  CLUS_2               50                 55
  CLUS_3               29                 83
D57V3, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               30                 43
  CLUS_2               17                 25
  CLUS_3               18                 29
D57V4, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               21                 32
  CLUS_2               34                 37
  CLUS_3               10                 28
D57V5, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               13                 31
  CLUS_2               38                 43
  CLUS_3               54                 31
  CLUS_4               15                 57
D57V6, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               36                 43
  CLUS_2               30                 85
  CLUS_3               54                 34
D57V7, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               57                 65
  CLUS_2               35                 53
  CLUS_3               27                 45
D57V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     79   40
  10P LOSS WILD-TYPE   97   66
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               79                 97
  CLUS_2               40                 66

Clustering(58) Variable = 10q loss mutation analysis
D58V1, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               36                 18
  CLUS_2               49                 46
  CLUS_3                6                 62
  CLUS_4               44                 27
D58V2, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               45                 26
  CLUS_2               57                 48
  CLUS_3               33                 79
D58V3, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               36                 37
  CLUS_2               17                 25
  CLUS_3               20                 27
D58V4, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               25                 28
  CLUS_2               36                 35
  CLUS_3               12                 26
D58V5, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               16                 28
  CLUS_2               41                 40
  CLUS_3               60                 25
  CLUS_4               18                 54
D58V6, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               37                 42
  CLUS_2               39                 76
  CLUS_3               59                 29
D58V7, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               61                 61
  CLUS_2               41                 47
  CLUS_3               32                 40
D58V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     86   48
  10Q LOSS WILD-TYPE   90   58
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               86                 90
  CLUS_2               48                 58

Clustering(59) Variable = 11p loss mutation analysis
D59V1, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                8                 46
  CLUS_2               16                 79
  CLUS_3                5                 63
  CLUS_4               34                 37
D59V2, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               22                 49
  CLUS_2               27                 78
  CLUS_3               14                 98
D59V3, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               20                 53
  CLUS_2                8                 34
  CLUS_3               11                 36
D59V4, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               10                 43
  CLUS_2               19                 52
  CLUS_3               10                 28
D59V5, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                9                 35
  CLUS_2               22                 59
  CLUS_3               23                 62
  CLUS_4                9                 63
D59V6, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               20                 59
  CLUS_2               22                 93
  CLUS_3               21                 67
D59V7, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               31                 91
  CLUS_2               13                 75
  CLUS_3               18                 54
D59V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     41   21
  11P LOSS WILD-TYPE  135   85
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               41                135
  CLUS_2               21                 85

Clustering(60) Variable = 11q loss mutation analysis
D60V1, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                6                 48
  CLUS_2               21                 74
  CLUS_3               11                 57
  CLUS_4               34                 37
D60V2, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               28                 43
  CLUS_2               24                 81
  CLUS_3               20                 92
D60V3, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               21                 52
  CLUS_2                9                 33
  CLUS_3               14                 33
D60V4, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               14                 39
  CLUS_2               20                 51
  CLUS_3               10                 28
D60V5, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               13                 31
  CLUS_2               25                 56
  CLUS_3               22                 63
  CLUS_4               12                 60
D60V6, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               23                 56
  CLUS_2               28                 87
  CLUS_3               21                 67
D60V7, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               33                 89
  CLUS_2               20                 68
  CLUS_3               18                 54
D60V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     45   26
  11Q LOSS WILD-TYPE  131   80
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               45                131
  CLUS_2               26                 80

Clustering(61) Variable = 12p loss mutation analysis
D61V1, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                2                 52
  CLUS_2               12                 83
  CLUS_3                3                 65
  CLUS_4                4                 67
D61V2, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                9                 62
  CLUS_2               11                 94
  CLUS_3                1                111
D61V3, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                7                 66
  CLUS_2                3                 39
  CLUS_3                3                 44
D61V4, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                7                 46
  CLUS_2                5                 66
  CLUS_3                1                 37
D61V5, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                4                 40
  CLUS_2                5                 76
  CLUS_3                9                 76
  CLUS_4                3                 69
D61V6, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                5                 74
  CLUS_2                5                110
  CLUS_3               11                 77
D61V7, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                9                113
  CLUS_2                5                 83
  CLUS_3                6                 66
D61V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     12    8
  12P LOSS WILD-TYPE  164   98
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               12                164
  CLUS_2                8                 98

Clustering(62) Variable = 12q loss mutation analysis
D62V1, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                5                 49
  CLUS_2               15                 80
  CLUS_3                3                 65
  CLUS_4                8                 63
D62V2, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               14                 57
  CLUS_2               15                 90
  CLUS_3                2                110
D62V3, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                8                 65
  CLUS_2                5                 37
  CLUS_3                5                 42
D62V4, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                8                 45
  CLUS_2                7                 64
  CLUS_3                3                 35
D62V5, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                8                 36
  CLUS_2                6                 75
  CLUS_3               13                 72
  CLUS_4                4                 68
D62V6, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               12                 67
  CLUS_2                6                109
  CLUS_3               13                 75
D62V7, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               13                109
  CLUS_2                8                 80
  CLUS_3                9                 63
D62V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     21    9
  12Q LOSS WILD-TYPE  155   97
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               21                155
  CLUS_2                9                 97

Clustering(63) Variable = 13q loss mutation analysis
D63V1, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                6                 48
  CLUS_2                7                 88
  CLUS_3                6                 62
  CLUS_4               21                 50
D63V2, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                6                 65
  CLUS_2               17                 88
  CLUS_3               17                 95
D63V3, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               10                 63
  CLUS_2                6                 36
  CLUS_3                8                 39
D63V4, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               11                 42
  CLUS_2                9                 62
  CLUS_3                4                 34
D63V5, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                7                 37
  CLUS_2               11                 70
  CLUS_3               13                 72
  CLUS_4                9                 63
D63V6, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                8                 71
  CLUS_2               15                100
  CLUS_3               17                 71
D63V7, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               19                103
  CLUS_2               14                 74
  CLUS_3                7                 65
D63V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     26   14
  13Q LOSS WILD-TYPE  150   92
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               26                150
  CLUS_2               14                 92

Clustering(64) Variable = 14q loss mutation analysis
D64V1, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                6                 48
  CLUS_2               33                 62
  CLUS_3                1                 67
  CLUS_4               21                 50
D64V2, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               23                 48
  CLUS_2               22                 83
  CLUS_3               16                 96
D64V3, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               16                 57
  CLUS_2                8                 34
  CLUS_3               11                 36
D64V4, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               11                 42
  CLUS_2               14                 57
  CLUS_3               10                 28
D64V5, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                8                 36
  CLUS_2               12                 69
  CLUS_3               31                 54
  CLUS_4               10                 62
D64V6, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               16                 63
  CLUS_2               16                 99
  CLUS_3               29                 59
D64V7, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               27                 95
  CLUS_2               20                 68
  CLUS_3               12                 60
D64V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     38   21
  14Q LOSS WILD-TYPE  138   85
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               38                138
  CLUS_2               21                 85

Clustering(65) Variable = 15q loss mutation analysis
D65V1, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                2                 52
  CLUS_2               11                 84
  CLUS_3                0                 68
  CLUS_4                4                 67
D65V2, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                6                 65
  CLUS_2                9                 96
  CLUS_3                2                110
D65V3, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                6                 67
  CLUS_2                3                 39
  CLUS_3                0                 47
D65V4, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                4                 49
  CLUS_2                5                 66
  CLUS_3                0                 38
D65V5, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                2                 42
  CLUS_2                4                 77
  CLUS_3                7                 78
  CLUS_4                4                 68
D65V6, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                2                 77
  CLUS_2                6                109
  CLUS_3                9                 79
D65V7, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                9                113
  CLUS_2                6                 82
  CLUS_3                2                 70
D65V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     12    5
  15Q LOSS WILD-TYPE  164  101
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               12                164
  CLUS_2                5                101

Clustering(66) Variable = 16p loss mutation analysis
D66V1, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                5                 49
  CLUS_2               10                 85
  CLUS_3                0                 68
  CLUS_4                9                 62
D66V2, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               11                 60
  CLUS_2               11                 94
  CLUS_3                2                110
D66V3, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                9                 64
  CLUS_2                3                 39
  CLUS_3                1                 46
D66V4, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                4                 49
  CLUS_2                7                 64
  CLUS_3                2                 36
D66V5, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                2                 42
  CLUS_2               12                 69
  CLUS_3                7                 78
  CLUS_4                3                 69
D66V6, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                8                 71
  CLUS_2                9                106
  CLUS_3                7                 81
D66V7, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               15                107
  CLUS_2                4                 84
  CLUS_3                4                 68
D66V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     19    4
  16P LOSS WILD-TYPE  157  102
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               19                157
  CLUS_2                4                102

Clustering(67) Variable = 16q loss mutation analysis
D67V1, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                7                 47
  CLUS_2               24                 71
  CLUS_3                5                 63
  CLUS_4               21                 50
D67V2, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               22                 49
  CLUS_2               23                 82
  CLUS_3               12                100
D67V3, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               13                 60
  CLUS_2                8                 34
  CLUS_3                9                 38
D67V4, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                8                 45
  CLUS_2               13                 58
  CLUS_3                9                 29
D67V5, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                7                 37
  CLUS_2               26                 55
  CLUS_3               16                 69
  CLUS_4                7                 65
D67V6, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               18                 61
  CLUS_2               22                 93
  CLUS_3               16                 72
D67V7, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               32                 90
  CLUS_2               13                 75
  CLUS_3                9                 63
D67V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     41   13
  16Q LOSS WILD-TYPE  135   93
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               41                135
  CLUS_2               13                 93

Clustering(68) Variable = 17p loss mutation analysis
D68V1, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                9                 45
  CLUS_2               17                 78
  CLUS_3                8                 60
  CLUS_4               22                 49
D68V2, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               12                 59
  CLUS_2               26                 79
  CLUS_3               18                 94
D68V3, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               13                 60
  CLUS_2               10                 32
  CLUS_3                8                 39
D68V4, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               13                 40
  CLUS_2               12                 59
  CLUS_3                6                 32
D68V5, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                7                 37
  CLUS_2               23                 58
  CLUS_3               15                 70
  CLUS_4               11                 61
D68V6, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               17                 62
  CLUS_2               23                 92
  CLUS_3               16                 72
D68V7, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               26                 96
  CLUS_2               19                 69
  CLUS_3                9                 63
D68V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     37   17
  17P LOSS WILD-TYPE  139   89
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               37                139
  CLUS_2               17                 89

Clustering(69) Variable = 17q loss mutation analysis
D69V1, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                8                 46
  CLUS_2                8                 87
  CLUS_3                2                 66
  CLUS_4                9                 62
D69V2, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                8                 63
  CLUS_2               12                 93
  CLUS_3                7                105
D69V3, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                5                 68
  CLUS_2                5                 37
  CLUS_3                3                 44
D69V4, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                4                 49
  CLUS_2                7                 64
  CLUS_3                2                 36
D69V5, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                 42
  CLUS_2               12                 69
  CLUS_3                9                 76
  CLUS_4                4                 68
D69V6, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               10                 69
  CLUS_2                8                107
  CLUS_3                9                 79
D69V7, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               11                111
  CLUS_2                8                 80
  CLUS_3                6                 66
D69V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     16    9
  17Q LOSS WILD-TYPE  160   97
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               16                160
  CLUS_2                9                 97

Clustering(70) Variable = 18p loss mutation analysis
D70V1, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               11                 43
  CLUS_2               23                 72
  CLUS_3                4                 64
  CLUS_4               16                 55
D70V2, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               17                 54
  CLUS_2               26                 79
  CLUS_3               11                101
D70V3, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               11                 62
  CLUS_2               10                 32
  CLUS_3                8                 39
D70V4, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                8                 45
  CLUS_2               14                 57
  CLUS_3                7                 31
D70V5, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                6                 38
  CLUS_2               13                 68
  CLUS_3               29                 56
  CLUS_4                6                 66
D70V6, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               14                 65
  CLUS_2               10                105
  CLUS_3               30                 58
D70V7, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               22                100
  CLUS_2               14                 74
  CLUS_3               18                 54
D70V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     34   20
  18P LOSS WILD-TYPE  142   86
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               34                142
  CLUS_2               20                 86

Clustering(71) Variable = 18q loss mutation analysis
D71V1, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               10                 44
  CLUS_2               19                 76
  CLUS_3                4                 64
  CLUS_4               16                 55
D71V2, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               14                 57
  CLUS_2               24                 81
  CLUS_3               11                101
D71V3, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                9                 64
  CLUS_2               11                 31
  CLUS_3                6                 41
D71V4, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                5                 48
  CLUS_2               15                 56
  CLUS_3                6                 32
D71V5, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                4                 40
  CLUS_2               16                 65
  CLUS_3               22                 63
  CLUS_4                7                 65
D71V6, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               14                 65
  CLUS_2               11                104
  CLUS_3               24                 64
D71V7, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               19                103
  CLUS_2               16                 72
  CLUS_3               14                 58
D71V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     31   18
  18Q LOSS WILD-TYPE  145   88
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               31                145
  CLUS_2               18                 88

Clustering(72) Variable = 19p loss mutation analysis
D72V1, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                3                 51
  CLUS_2                5                 90
  CLUS_3                2                 66
  CLUS_4               12                 59
D72V2, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                3                 68
  CLUS_2               10                 95
  CLUS_3                9                103
D72V3, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                4                 69
  CLUS_2                6                 36
  CLUS_3                3                 44
D72V4, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                4                 49
  CLUS_2                7                 64
  CLUS_3                2                 36
D72V5, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                1                 43
  CLUS_2               12                 69
  CLUS_3                4                 81
  CLUS_4                5                 67
D72V6, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                4                 75
  CLUS_2               15                100
  CLUS_3                3                 85
D72V7, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                9                113
  CLUS_2                4                 84
  CLUS_3                9                 63
D72V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     15    7
  19P LOSS WILD-TYPE  161   99
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               15                161
  CLUS_2                7                 99

Clustering(73) Variable = 19q loss mutation analysis
D73V1, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                3                 51
  CLUS_2                5                 90
  CLUS_3                1                 67
  CLUS_4               13                 58
D73V2, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                3                 68
  CLUS_2               10                 95
  CLUS_3                9                103
D73V3, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                7                 66
  CLUS_2                4                 38
  CLUS_3                3                 44
D73V4, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                6                 47
  CLUS_2                6                 65
  CLUS_3                2                 36
D73V5, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                3                 41
  CLUS_2               10                 71
  CLUS_3                4                 81
  CLUS_4                5                 67
D73V6, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                4                 75
  CLUS_2               14                101
  CLUS_3                4                 84
D73V7, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                8                114
  CLUS_2                6                 82
  CLUS_3                8                 64
D73V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     16    6
  19Q LOSS WILD-TYPE  160  100
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               16                160
  CLUS_2                6                100

Clustering(74) Variable = 20p loss mutation analysis
D74V1, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                3                 51
  CLUS_2                6                 89
  CLUS_3                2                 66
  CLUS_4                3                 68
D74V2, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                5                 66
  CLUS_2                5                100
  CLUS_3                4                108
D74V3, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                 71
  CLUS_2                2                 40
  CLUS_3                4                 43
D74V4, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                3                 50
  CLUS_2                3                 68
  CLUS_3                2                 36
D74V5, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                4                 40
  CLUS_2                2                 79
  CLUS_3                4                 81
  CLUS_4                4                 68
D74V6, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                6                 73
  CLUS_2                3                112
  CLUS_3                5                 83
D74V7, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                8                114
  CLUS_2                5                 83
  CLUS_3                1                 71
D74V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      9    5
  20P LOSS WILD-TYPE  167  101
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                9                167
  CLUS_2                5                101

Clustering(75) Variable = 20q loss mutation analysis
D75V1, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                0                 54
  CLUS_2                3                 92
  CLUS_3                0                 68
  CLUS_4                0                 71
D75V2, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                2                 69
  CLUS_2                1                104
  CLUS_3                0                112
D75V3, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                161 
        TCGA-BF-A1PU         TCGA-BF-A1PX         TCGA-BF-A1PZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q4         TCGA-D3-A1Q5 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q6         TCGA-D3-A1Q7         TCGA-D3-A1Q8 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A1QA         TCGA-D3-A1QB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2JC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JN         TCGA-D3-A2JO 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D3-A2JP         TCGA-D3-A3C1         TCGA-D3-A3C3 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D3-A3CB         TCGA-D3-A3CE         TCGA-D9-A148 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D9-A149         TCGA-D9-A1JW         TCGA-D9-A1JX 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D9-A1X3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I2         TCGA-DA-A1I4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I8         TCGA-DA-A1IA 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DA-A1IB         TCGA-DA-A1IC         TCGA-EB-A1NK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A299 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A184         TCGA-EE-A185         TCGA-EE-A20C 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A29B         TCGA-EE-A29C 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A29E         TCGA-EE-A29G         TCGA-EE-A29H 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29M         TCGA-EE-A29N 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29R         TCGA-EE-A29S 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29V         TCGA-EE-A29W 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A2A0         TCGA-EE-A2A2         TCGA-EE-A2A6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A2GC         TCGA-EE-A2GH         TCGA-EE-A2GI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A2GK         TCGA-EE-A2GL         TCGA-EE-A2GP 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2GS         TCGA-EE-A2GT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A2GU         TCGA-EE-A2M5         TCGA-EE-A2M6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2MC         TCGA-EE-A2MD 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A2MI         TCGA-EE-A2MJ         TCGA-EE-A2MK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A2ML         TCGA-EE-A2MM         TCGA-EE-A2MN 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A2MP         TCGA-EE-A2MR         TCGA-EE-A2MS 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A2MT         TCGA-EE-A2MU         TCGA-EE-A3AA 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AC         TCGA-EE-A3AD 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A3AE         TCGA-EE-A3AF         TCGA-EE-A3AG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ER-A193         TCGA-ER-A194         TCGA-ER-A195 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ER-A196         TCGA-ER-A197         TCGA-ER-A198 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ER-A199         TCGA-ER-A19A         TCGA-ER-A19B 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19E         TCGA-ER-A19F 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ER-A19G         TCGA-ER-A19H         TCGA-ER-A19J 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ER-A19K         TCGA-ER-A19L         TCGA-ER-A19N 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ER-A19O         TCGA-ER-A19P         TCGA-ER-A19Q 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ER-A19S         TCGA-ER-A1A1         TCGA-ER-A2NB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ER-A2NC         TCGA-ER-A2ND         TCGA-ER-A2NE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ER-A2NG         TCGA-ER-A2NH         TCGA-FS-A1YW 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FS-A1Z0         TCGA-FS-A1Z3         TCGA-FS-A1Z4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZA         TCGA-FS-A1ZC         TCGA-FS-A1ZD 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZG         TCGA-FS-A1ZH         TCGA-FS-A1ZJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZK         TCGA-FS-A1ZM         TCGA-FS-A1ZN 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZQ         TCGA-FS-A1ZT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZU         TCGA-FS-A1ZZ         TCGA-GF-A2C7 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-GN-A261         TCGA-GN-A262         TCGA-GN-A263 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A269 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26C         TCGA-GN-A26D 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HR-A2OG         TCGA-HR-A2OH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D75V4, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                161 
        TCGA-BF-A1PU         TCGA-BF-A1PX         TCGA-BF-A1PZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q4         TCGA-D3-A1Q5 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q6         TCGA-D3-A1Q7         TCGA-D3-A1Q8 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A1QA         TCGA-D3-A1QB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2JC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JN         TCGA-D3-A2JO 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D3-A2JP         TCGA-D3-A3C1         TCGA-D3-A3C3 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D3-A3CB         TCGA-D3-A3CE         TCGA-D9-A148 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D9-A149         TCGA-D9-A1JW         TCGA-D9-A1JX 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D9-A1X3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I2         TCGA-DA-A1I4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I8         TCGA-DA-A1IA 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DA-A1IB         TCGA-DA-A1IC         TCGA-EB-A1NK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A299 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A184         TCGA-EE-A185         TCGA-EE-A20C 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A29B         TCGA-EE-A29C 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A29E         TCGA-EE-A29G         TCGA-EE-A29H 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29M         TCGA-EE-A29N 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29R         TCGA-EE-A29S 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29V         TCGA-EE-A29W 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A2A0         TCGA-EE-A2A2         TCGA-EE-A2A6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A2GC         TCGA-EE-A2GH         TCGA-EE-A2GI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A2GK         TCGA-EE-A2GL         TCGA-EE-A2GP 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2GS         TCGA-EE-A2GT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A2GU         TCGA-EE-A2M5         TCGA-EE-A2M6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2MC         TCGA-EE-A2MD 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A2MI         TCGA-EE-A2MJ         TCGA-EE-A2MK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A2ML         TCGA-EE-A2MM         TCGA-EE-A2MN 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A2MP         TCGA-EE-A2MR         TCGA-EE-A2MS 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A2MT         TCGA-EE-A2MU         TCGA-EE-A3AA 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AC         TCGA-EE-A3AD 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EE-A3AE         TCGA-EE-A3AF         TCGA-EE-A3AG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ER-A193         TCGA-ER-A194         TCGA-ER-A195 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ER-A196         TCGA-ER-A197         TCGA-ER-A198 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ER-A199         TCGA-ER-A19A         TCGA-ER-A19B 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19E         TCGA-ER-A19F 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ER-A19G         TCGA-ER-A19H         TCGA-ER-A19J 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ER-A19K         TCGA-ER-A19L         TCGA-ER-A19N 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ER-A19O         TCGA-ER-A19P         TCGA-ER-A19Q 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ER-A19S         TCGA-ER-A1A1         TCGA-ER-A2NB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ER-A2NC         TCGA-ER-A2ND         TCGA-ER-A2NE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ER-A2NG         TCGA-ER-A2NH         TCGA-FS-A1YW 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FS-A1Z0         TCGA-FS-A1Z3         TCGA-FS-A1Z4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZA         TCGA-FS-A1ZC         TCGA-FS-A1ZD 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZG         TCGA-FS-A1ZH         TCGA-FS-A1ZJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZK         TCGA-FS-A1ZM         TCGA-FS-A1ZN 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZQ         TCGA-FS-A1ZT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZU         TCGA-FS-A1ZZ         TCGA-GF-A2C7 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-GN-A261         TCGA-GN-A262         TCGA-GN-A263 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A269 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26C         TCGA-GN-A26D 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HR-A2OG         TCGA-HR-A2OH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D75V5, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                1                 43
  CLUS_2                1                 80
  CLUS_3                0                 85
  CLUS_4                1                 71
D75V6, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                2                 77
  CLUS_2                0                115
  CLUS_3                1                 87
D75V7, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                2                120
  CLUS_2                1                 87
  CLUS_3                0                 72
D75V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    1
  20Q LOSS WILD-TYPE  174  105
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                2                174
  CLUS_2                1                105

Clustering(76) Variable = 21q loss mutation analysis
D76V1, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                6                 48
  CLUS_2               13                 82
  CLUS_3                4                 64
  CLUS_4               10                 61
D76V2, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                8                 63
  CLUS_2               15                 90
  CLUS_3               10                102
D76V3, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               13                 60
  CLUS_2                4                 38
  CLUS_3                6                 41
D76V4, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                8                 45
  CLUS_2               11                 60
  CLUS_3                4                 34
D76V5, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                5                 39
  CLUS_2               10                 71
  CLUS_3               11                 74
  CLUS_4                6                 66
D76V6, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                8                 71
  CLUS_2               11                104
  CLUS_3               13                 75
D76V7, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               16                106
  CLUS_2                6                 82
  CLUS_3               11                 61
D76V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     19   14
  21Q LOSS WILD-TYPE  157   92
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               19                157
  CLUS_2               14                 92

Clustering(77) Variable = 22q loss mutation analysis
D77V1, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                5                 49
  CLUS_2               14                 81
  CLUS_3                1                 67
  CLUS_4                4                 67
D77V2, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                9                 62
  CLUS_2               11                 94
  CLUS_3                4                108
D77V3, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                4                 69
  CLUS_2                3                 39
  CLUS_3                7                 40
D77V4, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                4                 49
  CLUS_2                6                 65
  CLUS_3                4                 34
D77V5, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                3                 41
  CLUS_2                8                 73
  CLUS_3                8                 77
  CLUS_4                4                 68
D77V6, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                5                 74
  CLUS_2                7                108
  CLUS_3               11                 77
D77V7, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               13                109
  CLUS_2                6                 82
  CLUS_3                4                 68
D77V8, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     17    6
  22Q LOSS WILD-TYPE  159  100
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               17                159
  CLUS_2                6                100

Clustering(78) Variable = Xq loss mutation analysis
D78V1, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               2                52
  CLUS_2               4                91
  CLUS_3               0                68
  CLUS_4               3                68
D78V2, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               2                69
  CLUS_2               7                98
  CLUS_3               0               112
D78V3, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               5                68
  CLUS_2               1                41
  CLUS_3               1                46
D78V4, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               3                50
  CLUS_2               4                67
  CLUS_3               0                38
D78V5, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                44
  CLUS_2               4                77
  CLUS_3               4                81
  CLUS_4               1                71
D78V6, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               3                76
  CLUS_2               2               113
  CLUS_3               4                84
D78V7, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               5               117
  CLUS_2               0                88
  CLUS_3               4                68
D78V8, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      6    3
  XQ LOSS WILD-TYPE  170  103
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               6               170
  CLUS_2               3               103
                     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")
