
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/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/Correlate_Genomic_Events.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LAML-TB/6159622/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LAML-TB/6159589/LAML-TB.transferedmergedcluster.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ONLYSIG", "-oT=LAML-TB", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=LAML-TB"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LAML-TB/6159589/LAML-TB.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LAML-TB/6159622/transformed.cor.cli.txt"

nPatients in clinical file=200, in cluster file=191, common to both=191
[1] "Reduce the number of clustering variables from 40 to 30."
[1]  30 191
[1] "1P MUTATION ANALYSIS"
[1] 3
  1P MUTATED 1P WILD-TYPE 
           3          188 
  1P MUTATED 1P WILD-TYPE 
           3          188 
[1] "3P MUTATION ANALYSIS"
[1] 3
  3P MUTATED 3P WILD-TYPE 
           4          187 
  3P MUTATED 3P WILD-TYPE 
           4          187 
[1] "3Q MUTATION ANALYSIS"
[1] 3
  3Q MUTATED 3Q WILD-TYPE 
           4          187 
  3Q MUTATED 3Q WILD-TYPE 
           4          187 
[1] "4P MUTATION ANALYSIS"
[1] 3
  4P MUTATED 4P WILD-TYPE 
           6          185 
  4P MUTATED 4P WILD-TYPE 
           6          185 
[1] "4Q MUTATION ANALYSIS"
[1] 3
  4Q MUTATED 4Q WILD-TYPE 
           6          185 
  4Q MUTATED 4Q WILD-TYPE 
           6          185 
[1] "5P MUTATION ANALYSIS"
[1] 3
  5P MUTATED 5P WILD-TYPE 
           3          188 
  5P MUTATED 5P WILD-TYPE 
           3          188 
[1] "5Q MUTATION ANALYSIS"
[1] 3
  5Q MUTATED 5Q WILD-TYPE 
           6          185 
  5Q MUTATED 5Q WILD-TYPE 
           6          185 
[1] "7P MUTATION ANALYSIS"
[1] 3
  7P MUTATED 7P WILD-TYPE 
          18          173 
  7P MUTATED 7P WILD-TYPE 
          18          173 
[1] "7Q MUTATION ANALYSIS"
[1] 3
  7Q MUTATED 7Q WILD-TYPE 
          20          171 
  7Q MUTATED 7Q WILD-TYPE 
          20          171 
[1] "8P MUTATION ANALYSIS"
[1] 3
  8P MUTATED 8P WILD-TYPE 
          23          168 
  8P MUTATED 8P WILD-TYPE 
          23          168 
[1] "8Q MUTATION ANALYSIS"
[1] 3
  8Q MUTATED 8Q WILD-TYPE 
          23          168 
  8Q MUTATED 8Q WILD-TYPE 
          23          168 
[1] "9P MUTATION ANALYSIS"
[1] 3
  9P MUTATED 9P WILD-TYPE 
           3          188 
  9P MUTATED 9P WILD-TYPE 
           3          188 
[1] "9Q MUTATION ANALYSIS"
[1] 3
  9Q MUTATED 9Q WILD-TYPE 
           3          188 
  9Q MUTATED 9Q WILD-TYPE 
           3          188 
[1] "10P MUTATION ANALYSIS"
[1] 3
  10P MUTATED 10P WILD-TYPE 
            3           188 
  10P MUTATED 10P WILD-TYPE 
            3           188 
[1] "10Q MUTATION ANALYSIS"
[1] 3
  10Q MUTATED 10Q WILD-TYPE 
            4           187 
  10Q MUTATED 10Q WILD-TYPE 
            4           187 
[1] "11P MUTATION ANALYSIS"
[1] 3
  11P MUTATED 11P WILD-TYPE 
            6           185 
  11P MUTATED 11P WILD-TYPE 
            6           185 
[1] "11Q MUTATION ANALYSIS"
[1] 3
  11Q MUTATED 11Q WILD-TYPE 
            7           184 
  11Q MUTATED 11Q WILD-TYPE 
            7           184 
[1] "12P MUTATION ANALYSIS"
[1] 3
  12P MUTATED 12P WILD-TYPE 
            4           187 
  12P MUTATED 12P WILD-TYPE 
            4           187 
[1] "13Q MUTATION ANALYSIS"
[1] 3
  13Q MUTATED 13Q WILD-TYPE 
            7           184 
  13Q MUTATED 13Q WILD-TYPE 
            7           184 
[1] "15Q MUTATION ANALYSIS"
[1] 3
  15Q MUTATED 15Q WILD-TYPE 
            4           187 
  15Q MUTATED 15Q WILD-TYPE 
            4           187 
[1] "16Q MUTATION ANALYSIS"
[1] 3
  16Q MUTATED 16Q WILD-TYPE 
            4           187 
  16Q MUTATED 16Q WILD-TYPE 
            4           187 
[1] "17P MUTATION ANALYSIS"
[1] 3
  17P MUTATED 17P WILD-TYPE 
           13           178 
  17P MUTATED 17P WILD-TYPE 
           13           178 
[1] "17Q MUTATION ANALYSIS"
[1] 3
  17Q MUTATED 17Q WILD-TYPE 
           10           181 
  17Q MUTATED 17Q WILD-TYPE 
           10           181 
[1] "18P MUTATION ANALYSIS"
[1] 3
  18P MUTATED 18P WILD-TYPE 
            5           186 
  18P MUTATED 18P WILD-TYPE 
            5           186 
[1] "18Q MUTATION ANALYSIS"
[1] 3
  18Q MUTATED 18Q WILD-TYPE 
            4           187 
  18Q MUTATED 18Q WILD-TYPE 
            4           187 
[1] "19P MUTATION ANALYSIS"
[1] 3
  19P MUTATED 19P WILD-TYPE 
            9           182 
  19P MUTATED 19P WILD-TYPE 
            9           182 
[1] "19Q MUTATION ANALYSIS"
[1] 3
  19Q MUTATED 19Q WILD-TYPE 
            9           182 
  19Q MUTATED 19Q WILD-TYPE 
            9           182 
[1] "21Q MUTATION ANALYSIS"
[1] 3
  21Q MUTATED 21Q WILD-TYPE 
           10           181 
  21Q MUTATED 21Q WILD-TYPE 
           10           181 
[1] "22Q MUTATION ANALYSIS"
[1] 3
  22Q MUTATED 22Q WILD-TYPE 
           11           180 
  22Q MUTATED 22Q WILD-TYPE 
           11           180 
[1] "XQ MUTATION ANALYSIS"
[1] 3
  XQ MUTATED XQ WILD-TYPE 
           8          183 
  XQ MUTATED XQ WILD-TYPE 
           8          183 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 6 rows and 191 columns.

Variable 1:'CN_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 191 columns, 0 survival variables, and 6 non-survival variables.
CN_CNMF, nv=4, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=5, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=2, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P MUTATED        0      2      1      0
  1P WILD-TYPE    147     12     26      3
D1V1, multiclass
        clus
vv       1P MUTATED 1P WILD-TYPE
  CLUS_1          0          147
  CLUS_2          2           12
  CLUS_3          1           26
  CLUS_4          0            3
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  1P MUTATED        0      0      3      0      0
  1P WILD-TYPE     46     44     58     14     20
D1V2, multiclass
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  1P MUTATED        3      0      0
  1P WILD-TYPE     67     52     44
D1V3, multiclass
        clus
vv       1P MUTATED 1P WILD-TYPE
  CLUS_1          3           67
  CLUS_2          0           52
  CLUS_3          0           44
D1V4, binary
              cls
clus             0   1
  1P MUTATED     0   3
  1P WILD-TYPE  56 107
[1] "tbl2"
              cls
clus           [,1] [,2]
  1P MUTATED      0    3
  1P WILD-TYPE   56  107
        clus
vv       1P MUTATED 1P WILD-TYPE
  CLUS_1          0           56
  CLUS_2          3          107
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P MUTATED        0      2      0      1
  1P WILD-TYPE     58     35     41     42
D1V5, multiclass
        clus
vv       1P MUTATED 1P WILD-TYPE
  CLUS_1          0           58
  CLUS_2          2           35
  CLUS_3          0           41
  CLUS_4          1           42
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  1P MUTATED        2      0      1
  1P WILD-TYPE     33     79     64
D1V6, multiclass
        clus
vv       1P MUTATED 1P WILD-TYPE
  CLUS_1          2           33
  CLUS_2          0           79
  CLUS_3          1           64

Clustering(2) Variable = 3P MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P MUTATED        0      0      4      0
  3P WILD-TYPE    147     14     23      3
D2V1, multiclass
        clus
vv       3P MUTATED 3P WILD-TYPE
  CLUS_1          0          147
  CLUS_2          0           14
  CLUS_3          4           23
  CLUS_4          0            3
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  3P MUTATED        0      0      3      0      0
  3P WILD-TYPE     46     44     58     14     20
D2V2, multiclass
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  3P MUTATED        3      1      0
  3P WILD-TYPE     67     51     44
D2V3, multiclass
        clus
vv       3P MUTATED 3P WILD-TYPE
  CLUS_1          3           67
  CLUS_2          1           51
  CLUS_3          0           44
D2V4, binary
              cls
clus             0   1
  3P MUTATED     2   2
  3P WILD-TYPE  54 108
[1] "tbl2"
              cls
clus           [,1] [,2]
  3P MUTATED      2    2
  3P WILD-TYPE   54  108
        clus
vv       3P MUTATED 3P WILD-TYPE
  CLUS_1          2           54
  CLUS_2          2          108
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P MUTATED        0      3      1      0
  3P WILD-TYPE     58     34     40     43
D2V5, multiclass
        clus
vv       3P MUTATED 3P WILD-TYPE
  CLUS_1          0           58
  CLUS_2          3           34
  CLUS_3          1           40
  CLUS_4          0           43
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  3P MUTATED        3      0      1
  3P WILD-TYPE     32     79     64
D2V6, multiclass
        clus
vv       3P MUTATED 3P WILD-TYPE
  CLUS_1          3           32
  CLUS_2          0           79
  CLUS_3          1           64

Clustering(3) Variable = 3Q MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q MUTATED        0      0      4      0
  3Q WILD-TYPE    147     14     23      3
D3V1, multiclass
        clus
vv       3Q MUTATED 3Q WILD-TYPE
  CLUS_1          0          147
  CLUS_2          0           14
  CLUS_3          4           23
  CLUS_4          0            3
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  3Q MUTATED        0      0      3      0      0
  3Q WILD-TYPE     46     44     58     14     20
D3V2, multiclass
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  3Q MUTATED        3      1      0
  3Q WILD-TYPE     67     51     44
D3V3, multiclass
        clus
vv       3Q MUTATED 3Q WILD-TYPE
  CLUS_1          3           67
  CLUS_2          1           51
  CLUS_3          0           44
D3V4, binary
              cls
clus             0   1
  3Q MUTATED     2   2
  3Q WILD-TYPE  54 108
[1] "tbl2"
              cls
clus           [,1] [,2]
  3Q MUTATED      2    2
  3Q WILD-TYPE   54  108
        clus
vv       3Q MUTATED 3Q WILD-TYPE
  CLUS_1          2           54
  CLUS_2          2          108
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q MUTATED        0      3      1      0
  3Q WILD-TYPE     58     34     40     43
D3V5, multiclass
        clus
vv       3Q MUTATED 3Q WILD-TYPE
  CLUS_1          0           58
  CLUS_2          3           34
  CLUS_3          1           40
  CLUS_4          0           43
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  3Q MUTATED        3      0      1
  3Q WILD-TYPE     32     79     64
D3V6, multiclass
        clus
vv       3Q MUTATED 3Q WILD-TYPE
  CLUS_1          3           32
  CLUS_2          0           79
  CLUS_3          1           64

Clustering(4) Variable = 4P MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P MUTATED        1      0      5      0
  4P WILD-TYPE    146     14     22      3
D4V1, multiclass
        clus
vv       4P MUTATED 4P WILD-TYPE
  CLUS_1          1          146
  CLUS_2          0           14
  CLUS_3          5           22
  CLUS_4          0            3
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  4P MUTATED        2      0      2      0      2
  4P WILD-TYPE     44     44     59     14     18
D4V2, multiclass
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  4P MUTATED        2      1      1
  4P WILD-TYPE     68     51     43
D4V3, multiclass
        clus
vv       4P MUTATED 4P WILD-TYPE
  CLUS_1          2           68
  CLUS_2          1           51
  CLUS_3          1           43
D4V4, binary
              cls
clus             0   1
  4P MUTATED     1   3
  4P WILD-TYPE  55 107
[1] "tbl2"
              cls
clus           [,1] [,2]
  4P MUTATED      1    3
  4P WILD-TYPE   55  107
        clus
vv       4P MUTATED 4P WILD-TYPE
  CLUS_1          1           55
  CLUS_2          3          107
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P MUTATED        3      1      1      1
  4P WILD-TYPE     55     36     40     42
D4V5, multiclass
        clus
vv       4P MUTATED 4P WILD-TYPE
  CLUS_1          3           55
  CLUS_2          1           36
  CLUS_3          1           40
  CLUS_4          1           42
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  4P MUTATED        1      2      3
  4P WILD-TYPE     34     77     62
D4V6, multiclass
        clus
vv       4P MUTATED 4P WILD-TYPE
  CLUS_1          1           34
  CLUS_2          2           77
  CLUS_3          3           62

Clustering(5) Variable = 4Q MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4Q MUTATED        1      0      5      0
  4Q WILD-TYPE    146     14     22      3
D5V1, multiclass
        clus
vv       4Q MUTATED 4Q WILD-TYPE
  CLUS_1          1          146
  CLUS_2          0           14
  CLUS_3          5           22
  CLUS_4          0            3
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  4Q MUTATED        2      0      2      0      2
  4Q WILD-TYPE     44     44     59     14     18
D5V2, multiclass
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  4Q MUTATED        2      1      1
  4Q WILD-TYPE     68     51     43
D5V3, multiclass
        clus
vv       4Q MUTATED 4Q WILD-TYPE
  CLUS_1          2           68
  CLUS_2          1           51
  CLUS_3          1           43
D5V4, binary
              cls
clus             0   1
  4Q MUTATED     1   3
  4Q WILD-TYPE  55 107
[1] "tbl2"
              cls
clus           [,1] [,2]
  4Q MUTATED      1    3
  4Q WILD-TYPE   55  107
        clus
vv       4Q MUTATED 4Q WILD-TYPE
  CLUS_1          1           55
  CLUS_2          3          107
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4Q MUTATED        3      1      1      1
  4Q WILD-TYPE     55     36     40     42
D5V5, multiclass
        clus
vv       4Q MUTATED 4Q WILD-TYPE
  CLUS_1          3           55
  CLUS_2          1           36
  CLUS_3          1           40
  CLUS_4          1           42
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  4Q MUTATED        1      2      3
  4Q WILD-TYPE     34     77     62
D5V6, multiclass
        clus
vv       4Q MUTATED 4Q WILD-TYPE
  CLUS_1          1           34
  CLUS_2          2           77
  CLUS_3          3           62

Clustering(6) Variable = 5P MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5P MUTATED        1      0      2      0
  5P WILD-TYPE    146     14     25      3
D6V1, multiclass
        clus
vv       5P MUTATED 5P WILD-TYPE
  CLUS_1          1          146
  CLUS_2          0           14
  CLUS_3          2           25
  CLUS_4          0            3
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  5P MUTATED        1      0      2      0      0
  5P WILD-TYPE     45     44     59     14     20
D6V2, multiclass
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  5P MUTATED        2      1      0
  5P WILD-TYPE     68     51     44
D6V3, multiclass
        clus
vv       5P MUTATED 5P WILD-TYPE
  CLUS_1          2           68
  CLUS_2          1           51
  CLUS_3          0           44
D6V4, binary
              cls
clus             0   1
  5P MUTATED     1   2
  5P WILD-TYPE  55 108
[1] "tbl2"
              cls
clus           [,1] [,2]
  5P MUTATED      1    2
  5P WILD-TYPE   55  108
        clus
vv       5P MUTATED 5P WILD-TYPE
  CLUS_1          1           55
  CLUS_2          2          108
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5P MUTATED        0      2      1      0
  5P WILD-TYPE     58     35     40     43
D6V5, multiclass
        clus
vv       5P MUTATED 5P WILD-TYPE
  CLUS_1          0           58
  CLUS_2          2           35
  CLUS_3          1           40
  CLUS_4          0           43
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  5P MUTATED        2      1      0
  5P WILD-TYPE     33     78     65
D6V6, multiclass
        clus
vv       5P MUTATED 5P WILD-TYPE
  CLUS_1          2           33
  CLUS_2          1           78
  CLUS_3          0           65

Clustering(7) Variable = 5Q MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5Q MUTATED        0      0      6      0
  5Q WILD-TYPE    147     14     21      3
D7V1, multiclass
        clus
vv       5Q MUTATED 5Q WILD-TYPE
  CLUS_1          0          147
  CLUS_2          0           14
  CLUS_3          6           21
  CLUS_4          0            3
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  5Q MUTATED        0      0      6      0      0
  5Q WILD-TYPE     46     44     55     14     20
D7V2, multiclass
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  5Q MUTATED        4      1      0
  5Q WILD-TYPE     66     51     44
D7V3, multiclass
        clus
vv       5Q MUTATED 5Q WILD-TYPE
  CLUS_1          4           66
  CLUS_2          1           51
  CLUS_3          0           44
D7V4, binary
              cls
clus             0   1
  5Q MUTATED     1   4
  5Q WILD-TYPE  55 106
[1] "tbl2"
              cls
clus           [,1] [,2]
  5Q MUTATED      1    4
  5Q WILD-TYPE   55  106
        clus
vv       5Q MUTATED 5Q WILD-TYPE
  CLUS_1          1           55
  CLUS_2          4          106
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5Q MUTATED        0      3      2      0
  5Q WILD-TYPE     58     34     39     43
D7V5, multiclass
        clus
vv       5Q MUTATED 5Q WILD-TYPE
  CLUS_1          0           58
  CLUS_2          3           34
  CLUS_3          2           39
  CLUS_4          0           43
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  5Q MUTATED        3      0      2
  5Q WILD-TYPE     32     79     63
D7V6, multiclass
        clus
vv       5Q MUTATED 5Q WILD-TYPE
  CLUS_1          3           32
  CLUS_2          0           79
  CLUS_3          2           63

Clustering(8) Variable = 7P MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P MUTATED        7      0      9      2
  7P WILD-TYPE    140     14     18      1
D8V1, multiclass
        clus
vv       7P MUTATED 7P WILD-TYPE
  CLUS_1          7          140
  CLUS_2          0           14
  CLUS_3          9           18
  CLUS_4          2            1
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  7P MUTATED        1      0     15      1      1
  7P WILD-TYPE     45     44     46     13     19
D8V2, multiclass
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  7P MUTATED       13      0      3
  7P WILD-TYPE     57     52     41
D8V3, multiclass
        clus
vv       7P MUTATED 7P WILD-TYPE
  CLUS_1         13           57
  CLUS_2          0           52
  CLUS_3          3           41
D8V4, binary
              cls
clus            0  1
  7P MUTATED    0 16
  7P WILD-TYPE 56 94
[1] "tbl2"
              cls
clus           [,1] [,2]
  7P MUTATED      0   16
  7P WILD-TYPE   56   94
        clus
vv       7P MUTATED 7P WILD-TYPE
  CLUS_1          0           56
  CLUS_2         16           94
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P MUTATED        1     10      3      4
  7P WILD-TYPE     57     27     38     39
D8V5, multiclass
        clus
vv       7P MUTATED 7P WILD-TYPE
  CLUS_1          1           57
  CLUS_2         10           27
  CLUS_3          3           38
  CLUS_4          4           39
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  7P MUTATED       11      2      5
  7P WILD-TYPE     24     77     60
D8V6, multiclass
        clus
vv       7P MUTATED 7P WILD-TYPE
  CLUS_1         11           24
  CLUS_2          2           77
  CLUS_3          5           60

Clustering(9) Variable = 7Q MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q MUTATED        8      0     10      2
  7Q WILD-TYPE    139     14     17      1
D9V1, multiclass
        clus
vv       7Q MUTATED 7Q WILD-TYPE
  CLUS_1          8          139
  CLUS_2          0           14
  CLUS_3         10           17
  CLUS_4          2            1
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  7Q MUTATED        1      0     17      1      1
  7Q WILD-TYPE     45     44     44     13     19
D9V2, multiclass
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  7Q MUTATED       13      1      3
  7Q WILD-TYPE     57     51     41
D9V3, multiclass
        clus
vv       7Q MUTATED 7Q WILD-TYPE
  CLUS_1         13           57
  CLUS_2          1           51
  CLUS_3          3           41
D9V4, binary
              cls
clus            0  1
  7Q MUTATED    1 16
  7Q WILD-TYPE 55 94
[1] "tbl2"
              cls
clus           [,1] [,2]
  7Q MUTATED      1   16
  7Q WILD-TYPE   55   94
        clus
vv       7Q MUTATED 7Q WILD-TYPE
  CLUS_1          1           55
  CLUS_2         16           94
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q MUTATED        1     10      4      4
  7Q WILD-TYPE     57     27     37     39
D9V5, multiclass
        clus
vv       7Q MUTATED 7Q WILD-TYPE
  CLUS_1          1           57
  CLUS_2         10           27
  CLUS_3          4           37
  CLUS_4          4           39
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  7Q MUTATED       11      2      6
  7Q WILD-TYPE     24     77     59
D9V6, multiclass
        clus
vv       7Q MUTATED 7Q WILD-TYPE
  CLUS_1         11           24
  CLUS_2          2           77
  CLUS_3          6           59

Clustering(10) Variable = 8P MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P MUTATED       11      1     10      1
  8P WILD-TYPE    136     13     17      2
D10V1, multiclass
        clus
vv       8P MUTATED 8P WILD-TYPE
  CLUS_1         11          136
  CLUS_2          1           13
  CLUS_3         10           17
  CLUS_4          1            2
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  8P MUTATED        2      1     17      0      2
  8P WILD-TYPE     44     43     44     14     18
D10V2, multiclass
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  8P MUTATED       14      2      3
  8P WILD-TYPE     56     50     41
D10V3, multiclass
        clus
vv       8P MUTATED 8P WILD-TYPE
  CLUS_1         14           56
  CLUS_2          2           50
  CLUS_3          3           41
D10V4, binary
              cls
clus            0  1
  8P MUTATED    1 18
  8P WILD-TYPE 55 92
[1] "tbl2"
              cls
clus           [,1] [,2]
  8P MUTATED      1   18
  8P WILD-TYPE   55   92
        clus
vv       8P MUTATED 8P WILD-TYPE
  CLUS_1          1           55
  CLUS_2         18           92
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P MUTATED        2     10      3      7
  8P WILD-TYPE     56     27     38     36
D10V5, multiclass
        clus
vv       8P MUTATED 8P WILD-TYPE
  CLUS_1          2           56
  CLUS_2         10           27
  CLUS_3          3           38
  CLUS_4          7           36
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  8P MUTATED        9      7      6
  8P WILD-TYPE     26     72     59
D10V6, multiclass
        clus
vv       8P MUTATED 8P WILD-TYPE
  CLUS_1          9           26
  CLUS_2          7           72
  CLUS_3          6           59

Clustering(11) Variable = 8Q MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q MUTATED       12      1     10      0
  8Q WILD-TYPE    135     13     17      3
D11V1, multiclass
        clus
vv       8Q MUTATED 8Q WILD-TYPE
  CLUS_1         12          135
  CLUS_2          1           13
  CLUS_3         10           17
  CLUS_4          0            3
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  8Q MUTATED        2      2     16      0      2
  8Q WILD-TYPE     44     42     45     14     18
D11V2, multiclass
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  8Q MUTATED       14      2      3
  8Q WILD-TYPE     56     50     41
D11V3, multiclass
        clus
vv       8Q MUTATED 8Q WILD-TYPE
  CLUS_1         14           56
  CLUS_2          2           50
  CLUS_3          3           41
D11V4, binary
              cls
clus            0  1
  8Q MUTATED    1 18
  8Q WILD-TYPE 55 92
[1] "tbl2"
              cls
clus           [,1] [,2]
  8Q MUTATED      1   18
  8Q WILD-TYPE   55   92
        clus
vv       8Q MUTATED 8Q WILD-TYPE
  CLUS_1          1           55
  CLUS_2         18           92
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q MUTATED        2      9      3      8
  8Q WILD-TYPE     56     28     38     35
D11V5, multiclass
        clus
vv       8Q MUTATED 8Q WILD-TYPE
  CLUS_1          2           56
  CLUS_2          9           28
  CLUS_3          3           38
  CLUS_4          8           35
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  8Q MUTATED        8      7      7
  8Q WILD-TYPE     27     72     58
D11V6, multiclass
        clus
vv       8Q MUTATED 8Q WILD-TYPE
  CLUS_1          8           27
  CLUS_2          7           72
  CLUS_3          7           58

Clustering(12) Variable = 9P MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P MUTATED        1      0      2      0
  9P WILD-TYPE    146     14     25      3
D12V1, multiclass
        clus
vv       9P MUTATED 9P WILD-TYPE
  CLUS_1          1          146
  CLUS_2          0           14
  CLUS_3          2           25
  CLUS_4          0            3
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  9P MUTATED        0      0      3      0      0
  9P WILD-TYPE     46     44     58     14     20
D12V2, multiclass
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  9P MUTATED        3      0      0
  9P WILD-TYPE     67     52     44
D12V3, multiclass
        clus
vv       9P MUTATED 9P WILD-TYPE
  CLUS_1          3           67
  CLUS_2          0           52
  CLUS_3          0           44
D12V4, binary
              cls
clus             0   1
  9P MUTATED     0   3
  9P WILD-TYPE  56 107
[1] "tbl2"
              cls
clus           [,1] [,2]
  9P MUTATED      0    3
  9P WILD-TYPE   56  107
        clus
vv       9P MUTATED 9P WILD-TYPE
  CLUS_1          0           56
  CLUS_2          3          107
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P MUTATED        0      2      1      0
  9P WILD-TYPE     58     35     40     43
D12V5, multiclass
        clus
vv       9P MUTATED 9P WILD-TYPE
  CLUS_1          0           58
  CLUS_2          2           35
  CLUS_3          1           40
  CLUS_4          0           43
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  9P MUTATED        2      0      1
  9P WILD-TYPE     33     79     64
D12V6, multiclass
        clus
vv       9P MUTATED 9P WILD-TYPE
  CLUS_1          2           33
  CLUS_2          0           79
  CLUS_3          1           64

Clustering(13) Variable = 9Q MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9Q MUTATED        1      0      2      0
  9Q WILD-TYPE    146     14     25      3
D13V1, multiclass
        clus
vv       9Q MUTATED 9Q WILD-TYPE
  CLUS_1          1          146
  CLUS_2          0           14
  CLUS_3          2           25
  CLUS_4          0            3
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  9Q MUTATED        0      0      3      0      0
  9Q WILD-TYPE     46     44     58     14     20
D13V2, multiclass
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  9Q MUTATED        3      0      0
  9Q WILD-TYPE     67     52     44
D13V3, multiclass
        clus
vv       9Q MUTATED 9Q WILD-TYPE
  CLUS_1          3           67
  CLUS_2          0           52
  CLUS_3          0           44
D13V4, binary
              cls
clus             0   1
  9Q MUTATED     0   3
  9Q WILD-TYPE  56 107
[1] "tbl2"
              cls
clus           [,1] [,2]
  9Q MUTATED      0    3
  9Q WILD-TYPE   56  107
        clus
vv       9Q MUTATED 9Q WILD-TYPE
  CLUS_1          0           56
  CLUS_2          3          107
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9Q MUTATED        0      2      1      0
  9Q WILD-TYPE     58     35     40     43
D13V5, multiclass
        clus
vv       9Q MUTATED 9Q WILD-TYPE
  CLUS_1          0           58
  CLUS_2          2           35
  CLUS_3          1           40
  CLUS_4          0           43
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  9Q MUTATED        2      0      1
  9Q WILD-TYPE     33     79     64
D13V6, multiclass
        clus
vv       9Q MUTATED 9Q WILD-TYPE
  CLUS_1          2           33
  CLUS_2          0           79
  CLUS_3          1           64

Clustering(14) Variable = 10P MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10P MUTATED        0      1      2      0
  10P WILD-TYPE    147     13     25      3
D14V1, multiclass
        clus
vv       10P MUTATED 10P WILD-TYPE
  CLUS_1           0           147
  CLUS_2           1            13
  CLUS_3           2            25
  CLUS_4           0             3
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  10P MUTATED        0      0      3      0      0
  10P WILD-TYPE     46     44     58     14     20
D14V2, multiclass
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  10P MUTATED        3      0      0
  10P WILD-TYPE     67     52     44
D14V3, multiclass
        clus
vv       10P MUTATED 10P WILD-TYPE
  CLUS_1           3            67
  CLUS_2           0            52
  CLUS_3           0            44
D14V4, binary
               cls
clus              0   1
  10P MUTATED     0   3
  10P WILD-TYPE  56 107
[1] "tbl2"
               cls
clus            [,1] [,2]
  10P MUTATED      0    3
  10P WILD-TYPE   56  107
        clus
vv       10P MUTATED 10P WILD-TYPE
  CLUS_1           0            56
  CLUS_2           3           107
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10P MUTATED        0      1      1      1
  10P WILD-TYPE     58     36     40     42
D14V5, multiclass
        clus
vv       10P MUTATED 10P WILD-TYPE
  CLUS_1           0            58
  CLUS_2           1            36
  CLUS_3           1            40
  CLUS_4           1            42
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  10P MUTATED        1      0      2
  10P WILD-TYPE     34     79     63
D14V6, multiclass
        clus
vv       10P MUTATED 10P WILD-TYPE
  CLUS_1           1            34
  CLUS_2           0            79
  CLUS_3           2            63

Clustering(15) Variable = 10Q MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10Q MUTATED        0      1      3      0
  10Q WILD-TYPE    147     13     24      3
D15V1, multiclass
        clus
vv       10Q MUTATED 10Q WILD-TYPE
  CLUS_1           0           147
  CLUS_2           1            13
  CLUS_3           3            24
  CLUS_4           0             3
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  10Q MUTATED        0      0      4      0      0
  10Q WILD-TYPE     46     44     57     14     20
D15V2, multiclass
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  10Q MUTATED        4      0      0
  10Q WILD-TYPE     66     52     44
D15V3, multiclass
        clus
vv       10Q MUTATED 10Q WILD-TYPE
  CLUS_1           4            66
  CLUS_2           0            52
  CLUS_3           0            44
D15V4, binary
               cls
clus              0   1
  10Q MUTATED     0   4
  10Q WILD-TYPE  56 106
[1] "tbl2"
               cls
clus            [,1] [,2]
  10Q MUTATED      0    4
  10Q WILD-TYPE   56  106
        clus
vv       10Q MUTATED 10Q WILD-TYPE
  CLUS_1           0            56
  CLUS_2           4           106
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10Q MUTATED        0      2      1      1
  10Q WILD-TYPE     58     35     40     42
D15V5, multiclass
        clus
vv       10Q MUTATED 10Q WILD-TYPE
  CLUS_1           0            58
  CLUS_2           2            35
  CLUS_3           1            40
  CLUS_4           1            42
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  10Q MUTATED        2      0      2
  10Q WILD-TYPE     33     79     63
D15V6, multiclass
        clus
vv       10Q MUTATED 10Q WILD-TYPE
  CLUS_1           2            33
  CLUS_2           0            79
  CLUS_3           2            63

Clustering(16) Variable = 11P MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P MUTATED        0      3      3      0
  11P WILD-TYPE    147     11     24      3
D16V1, multiclass
        clus
vv       11P MUTATED 11P WILD-TYPE
  CLUS_1           0           147
  CLUS_2           3            11
  CLUS_3           3            24
  CLUS_4           0             3
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11P MUTATED        0      0      6      0      0
  11P WILD-TYPE     46     44     55     14     20
D16V2, multiclass
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  11P MUTATED        5      1      0
  11P WILD-TYPE     65     51     44
D16V3, multiclass
        clus
vv       11P MUTATED 11P WILD-TYPE
  CLUS_1           5            65
  CLUS_2           1            51
  CLUS_3           0            44
D16V4, binary
               cls
clus              0   1
  11P MUTATED     1   5
  11P WILD-TYPE  55 105
[1] "tbl2"
               cls
clus            [,1] [,2]
  11P MUTATED      1    5
  11P WILD-TYPE   55  105
        clus
vv       11P MUTATED 11P WILD-TYPE
  CLUS_1           1            55
  CLUS_2           5           105
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P MUTATED        1      3      0      2
  11P WILD-TYPE     57     34     41     41
D16V5, multiclass
        clus
vv       11P MUTATED 11P WILD-TYPE
  CLUS_1           1            57
  CLUS_2           3            34
  CLUS_3           0            41
  CLUS_4           2            41
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  11P MUTATED        3      1      2
  11P WILD-TYPE     32     78     63
D16V6, multiclass
        clus
vv       11P MUTATED 11P WILD-TYPE
  CLUS_1           3            32
  CLUS_2           1            78
  CLUS_3           2            63

Clustering(17) Variable = 11Q MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q MUTATED        0      4      3      0
  11Q WILD-TYPE    147     10     24      3
D17V1, multiclass
        clus
vv       11Q MUTATED 11Q WILD-TYPE
  CLUS_1           0           147
  CLUS_2           4            10
  CLUS_3           3            24
  CLUS_4           0             3
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11Q MUTATED        0      0      7      0      0
  11Q WILD-TYPE     46     44     54     14     20
D17V2, multiclass
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  11Q MUTATED        6      1      0
  11Q WILD-TYPE     64     51     44
D17V3, multiclass
        clus
vv       11Q MUTATED 11Q WILD-TYPE
  CLUS_1           6            64
  CLUS_2           1            51
  CLUS_3           0            44
D17V4, binary
               cls
clus              0   1
  11Q MUTATED     1   6
  11Q WILD-TYPE  55 104
[1] "tbl2"
               cls
clus            [,1] [,2]
  11Q MUTATED      1    6
  11Q WILD-TYPE   55  104
        clus
vv       11Q MUTATED 11Q WILD-TYPE
  CLUS_1           1            55
  CLUS_2           6           104
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q MUTATED        2      3      0      2
  11Q WILD-TYPE     56     34     41     41
D17V5, multiclass
        clus
vv       11Q MUTATED 11Q WILD-TYPE
  CLUS_1           2            56
  CLUS_2           3            34
  CLUS_3           0            41
  CLUS_4           2            41
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  11Q MUTATED        3      2      2
  11Q WILD-TYPE     32     77     63
D17V6, multiclass
        clus
vv       11Q MUTATED 11Q WILD-TYPE
  CLUS_1           3            32
  CLUS_2           2            77
  CLUS_3           2            63

Clustering(18) Variable = 12P MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P MUTATED        1      0      2      1
  12P WILD-TYPE    146     14     25      2
D18V1, multiclass
        clus
vv       12P MUTATED 12P WILD-TYPE
  CLUS_1           1           146
  CLUS_2           0            14
  CLUS_3           2            25
  CLUS_4           1             2
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  12P MUTATED        0      0      2      0      2
  12P WILD-TYPE     46     44     59     14     18
D18V2, multiclass
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  12P MUTATED        3      0      1
  12P WILD-TYPE     67     52     43
D18V3, multiclass
        clus
vv       12P MUTATED 12P WILD-TYPE
  CLUS_1           3            67
  CLUS_2           0            52
  CLUS_3           1            43
D18V4, binary
               cls
clus              0   1
  12P MUTATED     0   4
  12P WILD-TYPE  56 106
[1] "tbl2"
               cls
clus            [,1] [,2]
  12P MUTATED      0    4
  12P WILD-TYPE   56  106
        clus
vv       12P MUTATED 12P WILD-TYPE
  CLUS_1           0            56
  CLUS_2           4           106
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P MUTATED        1      2      1      0
  12P WILD-TYPE     57     35     40     43
D18V5, multiclass
        clus
vv       12P MUTATED 12P WILD-TYPE
  CLUS_1           1            57
  CLUS_2           2            35
  CLUS_3           1            40
  CLUS_4           0            43
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  12P MUTATED        2      0      2
  12P WILD-TYPE     33     79     63
D18V6, multiclass
        clus
vv       12P MUTATED 12P WILD-TYPE
  CLUS_1           2            33
  CLUS_2           0            79
  CLUS_3           2            63

Clustering(19) Variable = 13Q MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q MUTATED        2      1      4      0
  13Q WILD-TYPE    145     13     23      3
D19V1, multiclass
        clus
vv       13Q MUTATED 13Q WILD-TYPE
  CLUS_1           2           145
  CLUS_2           1            13
  CLUS_3           4            23
  CLUS_4           0             3
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  13Q MUTATED        0      0      7      0      0
  13Q WILD-TYPE     46     44     54     14     20
D19V2, multiclass
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  13Q MUTATED        6      1      0
  13Q WILD-TYPE     64     51     44
D19V3, multiclass
        clus
vv       13Q MUTATED 13Q WILD-TYPE
  CLUS_1           6            64
  CLUS_2           1            51
  CLUS_3           0            44
D19V4, binary
               cls
clus              0   1
  13Q MUTATED     0   7
  13Q WILD-TYPE  56 103
[1] "tbl2"
               cls
clus            [,1] [,2]
  13Q MUTATED      0    7
  13Q WILD-TYPE   56  103
        clus
vv       13Q MUTATED 13Q WILD-TYPE
  CLUS_1           0            56
  CLUS_2           7           103
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q MUTATED        1      2      2      2
  13Q WILD-TYPE     57     35     39     41
D19V5, multiclass
        clus
vv       13Q MUTATED 13Q WILD-TYPE
  CLUS_1           1            57
  CLUS_2           2            35
  CLUS_3           2            39
  CLUS_4           2            41
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  13Q MUTATED        2      1      4
  13Q WILD-TYPE     33     78     61
D19V6, multiclass
        clus
vv       13Q MUTATED 13Q WILD-TYPE
  CLUS_1           2            33
  CLUS_2           1            78
  CLUS_3           4            61

Clustering(20) Variable = 15Q MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q MUTATED        0      0      3      1
  15Q WILD-TYPE    147     14     24      2
D20V1, multiclass
        clus
vv       15Q MUTATED 15Q WILD-TYPE
  CLUS_1           0           147
  CLUS_2           0            14
  CLUS_3           3            24
  CLUS_4           1             2
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  15Q MUTATED        0      1      2      0      1
  15Q WILD-TYPE     46     43     59     14     19
D20V2, multiclass
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  15Q MUTATED        4      0      0
  15Q WILD-TYPE     66     52     44
D20V3, multiclass
        clus
vv       15Q MUTATED 15Q WILD-TYPE
  CLUS_1           4            66
  CLUS_2           0            52
  CLUS_3           0            44
D20V4, binary
               cls
clus              0   1
  15Q MUTATED     0   4
  15Q WILD-TYPE  56 106
[1] "tbl2"
               cls
clus            [,1] [,2]
  15Q MUTATED      0    4
  15Q WILD-TYPE   56  106
        clus
vv       15Q MUTATED 15Q WILD-TYPE
  CLUS_1           0            56
  CLUS_2           4           106
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q MUTATED        0      3      0      1
  15Q WILD-TYPE     58     34     41     42
D20V5, multiclass
        clus
vv       15Q MUTATED 15Q WILD-TYPE
  CLUS_1           0            58
  CLUS_2           3            34
  CLUS_3           0            41
  CLUS_4           1            42
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  15Q MUTATED        3      0      1
  15Q WILD-TYPE     32     79     64
D20V6, multiclass
        clus
vv       15Q MUTATED 15Q WILD-TYPE
  CLUS_1           3            32
  CLUS_2           0            79
  CLUS_3           1            64

Clustering(21) Variable = 16Q MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q MUTATED        0      0      4      0
  16Q WILD-TYPE    147     14     23      3
D21V1, multiclass
        clus
vv       16Q MUTATED 16Q WILD-TYPE
  CLUS_1           0           147
  CLUS_2           0            14
  CLUS_3           4            23
  CLUS_4           0             3
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  16Q MUTATED        0      0      4      0      0
  16Q WILD-TYPE     46     44     57     14     20
D21V2, multiclass
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  16Q MUTATED        2      1      0
  16Q WILD-TYPE     68     51     44
D21V3, multiclass
        clus
vv       16Q MUTATED 16Q WILD-TYPE
  CLUS_1           2            68
  CLUS_2           1            51
  CLUS_3           0            44
D21V4, binary
               cls
clus              0   1
  16Q MUTATED     1   2
  16Q WILD-TYPE  55 108
[1] "tbl2"
               cls
clus            [,1] [,2]
  16Q MUTATED      1    2
  16Q WILD-TYPE   55  108
        clus
vv       16Q MUTATED 16Q WILD-TYPE
  CLUS_1           1            55
  CLUS_2           2           108
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q MUTATED        0      3      1      0
  16Q WILD-TYPE     58     34     40     43
D21V5, multiclass
        clus
vv       16Q MUTATED 16Q WILD-TYPE
  CLUS_1           0            58
  CLUS_2           3            34
  CLUS_3           1            40
  CLUS_4           0            43
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  16Q MUTATED        3      0      1
  16Q WILD-TYPE     32     79     64
D21V6, multiclass
        clus
vv       16Q MUTATED 16Q WILD-TYPE
  CLUS_1           3            32
  CLUS_2           0            79
  CLUS_3           1            64

Clustering(22) Variable = 17P MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P MUTATED        0      0     13      0
  17P WILD-TYPE    147     14     14      3
D22V1, multiclass
        clus
vv       17P MUTATED 17P WILD-TYPE
  CLUS_1           0           147
  CLUS_2           0            14
  CLUS_3          13            14
  CLUS_4           0             3
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  17P MUTATED        0      1     10      0      2
  17P WILD-TYPE     46     43     51     14     18
D22V2, multiclass
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  17P MUTATED        9      2      2
  17P WILD-TYPE     61     50     42
D22V3, multiclass
        clus
vv       17P MUTATED 17P WILD-TYPE
  CLUS_1           9            61
  CLUS_2           2            50
  CLUS_3           2            42
D22V4, binary
               cls
clus             0  1
  17P MUTATED    1 12
  17P WILD-TYPE 55 98
[1] "tbl2"
               cls
clus            [,1] [,2]
  17P MUTATED      1   12
  17P WILD-TYPE   55   98
        clus
vv       17P MUTATED 17P WILD-TYPE
  CLUS_1           1            55
  CLUS_2          12            98
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P MUTATED        2      6      2      3
  17P WILD-TYPE     56     31     39     40
D22V5, multiclass
        clus
vv       17P MUTATED 17P WILD-TYPE
  CLUS_1           2            56
  CLUS_2           6            31
  CLUS_3           2            39
  CLUS_4           3            40
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  17P MUTATED        6      1      6
  17P WILD-TYPE     29     78     59
D22V6, multiclass
        clus
vv       17P MUTATED 17P WILD-TYPE
  CLUS_1           6            29
  CLUS_2           1            78
  CLUS_3           6            59

Clustering(23) Variable = 17Q MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q MUTATED        0      0     10      0
  17Q WILD-TYPE    147     14     17      3
D23V1, multiclass
        clus
vv       17Q MUTATED 17Q WILD-TYPE
  CLUS_1           0           147
  CLUS_2           0            14
  CLUS_3          10            17
  CLUS_4           0             3
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  17Q MUTATED        0      1      7      0      2
  17Q WILD-TYPE     46     43     54     14     18
D23V2, multiclass
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  17Q MUTATED        7      2      1
  17Q WILD-TYPE     63     50     43
D23V3, multiclass
        clus
vv       17Q MUTATED 17Q WILD-TYPE
  CLUS_1           7            63
  CLUS_2           2            50
  CLUS_3           1            43
D23V4, binary
               cls
clus              0   1
  17Q MUTATED     1   9
  17Q WILD-TYPE  55 101
[1] "tbl2"
               cls
clus            [,1] [,2]
  17Q MUTATED      1    9
  17Q WILD-TYPE   55  101
        clus
vv       17Q MUTATED 17Q WILD-TYPE
  CLUS_1           1            55
  CLUS_2           9           101
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q MUTATED        2      5      1      2
  17Q WILD-TYPE     56     32     40     41
D23V5, multiclass
        clus
vv       17Q MUTATED 17Q WILD-TYPE
  CLUS_1           2            56
  CLUS_2           5            32
  CLUS_3           1            40
  CLUS_4           2            41
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  17Q MUTATED        5      0      5
  17Q WILD-TYPE     30     79     60
D23V6, multiclass
        clus
vv       17Q MUTATED 17Q WILD-TYPE
  CLUS_1           5            30
  CLUS_2           0            79
  CLUS_3           5            60

Clustering(24) Variable = 18P MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P MUTATED        0      0      5      0
  18P WILD-TYPE    147     14     22      3
D24V1, multiclass
        clus
vv       18P MUTATED 18P WILD-TYPE
  CLUS_1           0           147
  CLUS_2           0            14
  CLUS_3           5            22
  CLUS_4           0             3
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  18P MUTATED        0      0      5      0      0
  18P WILD-TYPE     46     44     56     14     20
D24V2, multiclass
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  18P MUTATED        2      1      1
  18P WILD-TYPE     68     51     43
D24V3, multiclass
        clus
vv       18P MUTATED 18P WILD-TYPE
  CLUS_1           2            68
  CLUS_2           1            51
  CLUS_3           1            43
D24V4, binary
               cls
clus              0   1
  18P MUTATED     1   3
  18P WILD-TYPE  55 107
[1] "tbl2"
               cls
clus            [,1] [,2]
  18P MUTATED      1    3
  18P WILD-TYPE   55  107
        clus
vv       18P MUTATED 18P WILD-TYPE
  CLUS_1           1            55
  CLUS_2           3           107
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P MUTATED        0      2      1      1
  18P WILD-TYPE     58     35     40     42
D24V5, multiclass
        clus
vv       18P MUTATED 18P WILD-TYPE
  CLUS_1           0            58
  CLUS_2           2            35
  CLUS_3           1            40
  CLUS_4           1            42
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  18P MUTATED        2      1      1
  18P WILD-TYPE     33     78     64
D24V6, multiclass
        clus
vv       18P MUTATED 18P WILD-TYPE
  CLUS_1           2            33
  CLUS_2           1            78
  CLUS_3           1            64

Clustering(25) Variable = 18Q MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q MUTATED        0      0      4      0
  18Q WILD-TYPE    147     14     23      3
D25V1, multiclass
        clus
vv       18Q MUTATED 18Q WILD-TYPE
  CLUS_1           0           147
  CLUS_2           0            14
  CLUS_3           4            23
  CLUS_4           0             3
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  18Q MUTATED        0      0      4      0      0
  18Q WILD-TYPE     46     44     57     14     20
D25V2, multiclass
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  18Q MUTATED        3      1      0
  18Q WILD-TYPE     67     51     44
D25V3, multiclass
        clus
vv       18Q MUTATED 18Q WILD-TYPE
  CLUS_1           3            67
  CLUS_2           1            51
  CLUS_3           0            44
D25V4, binary
               cls
clus              0   1
  18Q MUTATED     1   3
  18Q WILD-TYPE  55 107
[1] "tbl2"
               cls
clus            [,1] [,2]
  18Q MUTATED      1    3
  18Q WILD-TYPE   55  107
        clus
vv       18Q MUTATED 18Q WILD-TYPE
  CLUS_1           1            55
  CLUS_2           3           107
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q MUTATED        0      2      2      0
  18Q WILD-TYPE     58     35     39     43
D25V5, multiclass
        clus
vv       18Q MUTATED 18Q WILD-TYPE
  CLUS_1           0            58
  CLUS_2           2            35
  CLUS_3           2            39
  CLUS_4           0            43
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  18Q MUTATED        2      0      2
  18Q WILD-TYPE     33     79     63
D25V6, multiclass
        clus
vv       18Q MUTATED 18Q WILD-TYPE
  CLUS_1           2            33
  CLUS_2           0            79
  CLUS_3           2            63

Clustering(26) Variable = 19P MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P MUTATED        0      2      7      0
  19P WILD-TYPE    147     12     20      3
D26V1, multiclass
        clus
vv       19P MUTATED 19P WILD-TYPE
  CLUS_1           0           147
  CLUS_2           2            12
  CLUS_3           7            20
  CLUS_4           0             3
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  19P MUTATED        2      1      5      0      1
  19P WILD-TYPE     44     43     56     14     19
D26V2, multiclass
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  19P MUTATED        5      2      1
  19P WILD-TYPE     65     50     43
D26V3, multiclass
        clus
vv       19P MUTATED 19P WILD-TYPE
  CLUS_1           5            65
  CLUS_2           2            50
  CLUS_3           1            43
D26V4, binary
               cls
clus              0   1
  19P MUTATED     2   6
  19P WILD-TYPE  54 104
[1] "tbl2"
               cls
clus            [,1] [,2]
  19P MUTATED      2    6
  19P WILD-TYPE   54  104
        clus
vv       19P MUTATED 19P WILD-TYPE
  CLUS_1           2            54
  CLUS_2           6           104
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P MUTATED        3      2      2      2
  19P WILD-TYPE     55     35     39     41
D26V5, multiclass
        clus
vv       19P MUTATED 19P WILD-TYPE
  CLUS_1           3            55
  CLUS_2           2            35
  CLUS_3           2            39
  CLUS_4           2            41
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  19P MUTATED        2      2      5
  19P WILD-TYPE     33     77     60
D26V6, multiclass
        clus
vv       19P MUTATED 19P WILD-TYPE
  CLUS_1           2            33
  CLUS_2           2            77
  CLUS_3           5            60

Clustering(27) Variable = 19Q MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q MUTATED        0      2      7      0
  19Q WILD-TYPE    147     12     20      3
D27V1, multiclass
        clus
vv       19Q MUTATED 19Q WILD-TYPE
  CLUS_1           0           147
  CLUS_2           2            12
  CLUS_3           7            20
  CLUS_4           0             3
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  19Q MUTATED        2      1      5      0      1
  19Q WILD-TYPE     44     43     56     14     19
D27V2, multiclass
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  19Q MUTATED        5      2      1
  19Q WILD-TYPE     65     50     43
D27V3, multiclass
        clus
vv       19Q MUTATED 19Q WILD-TYPE
  CLUS_1           5            65
  CLUS_2           2            50
  CLUS_3           1            43
D27V4, binary
               cls
clus              0   1
  19Q MUTATED     2   6
  19Q WILD-TYPE  54 104
[1] "tbl2"
               cls
clus            [,1] [,2]
  19Q MUTATED      2    6
  19Q WILD-TYPE   54  104
        clus
vv       19Q MUTATED 19Q WILD-TYPE
  CLUS_1           2            54
  CLUS_2           6           104
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q MUTATED        3      2      2      2
  19Q WILD-TYPE     55     35     39     41
D27V5, multiclass
        clus
vv       19Q MUTATED 19Q WILD-TYPE
  CLUS_1           3            55
  CLUS_2           2            35
  CLUS_3           2            39
  CLUS_4           2            41
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  19Q MUTATED        2      2      5
  19Q WILD-TYPE     33     77     60
D27V6, multiclass
        clus
vv       19Q MUTATED 19Q WILD-TYPE
  CLUS_1           2            33
  CLUS_2           2            77
  CLUS_3           5            60

Clustering(28) Variable = 21Q MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q MUTATED        1      0      9      0
  21Q WILD-TYPE    146     14     18      3
D28V1, multiclass
        clus
vv       21Q MUTATED 21Q WILD-TYPE
  CLUS_1           1           146
  CLUS_2           0            14
  CLUS_3           9            18
  CLUS_4           0             3
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  21Q MUTATED        1      0      7      0      1
  21Q WILD-TYPE     45     44     54     14     19
D28V2, multiclass
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  21Q MUTATED        7      1      0
  21Q WILD-TYPE     63     51     44
D28V3, multiclass
        clus
vv       21Q MUTATED 21Q WILD-TYPE
  CLUS_1           7            63
  CLUS_2           1            51
  CLUS_3           0            44
D28V4, binary
               cls
clus              0   1
  21Q MUTATED     2   6
  21Q WILD-TYPE  54 104
[1] "tbl2"
               cls
clus            [,1] [,2]
  21Q MUTATED      2    6
  21Q WILD-TYPE   54  104
        clus
vv       21Q MUTATED 21Q WILD-TYPE
  CLUS_1           2            54
  CLUS_2           6           104
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q MUTATED        1      3      5      0
  21Q WILD-TYPE     57     34     36     43
D28V5, multiclass
        clus
vv       21Q MUTATED 21Q WILD-TYPE
  CLUS_1           1            57
  CLUS_2           3            34
  CLUS_3           5            36
  CLUS_4           0            43
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  21Q MUTATED        3      1      5
  21Q WILD-TYPE     32     78     60
D28V6, multiclass
        clus
vv       21Q MUTATED 21Q WILD-TYPE
  CLUS_1           3            32
  CLUS_2           1            78
  CLUS_3           5            60

Clustering(29) Variable = 22Q MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  22Q MUTATED        2      2      7      0
  22Q WILD-TYPE    145     12     20      3
D29V1, multiclass
        clus
vv       22Q MUTATED 22Q WILD-TYPE
  CLUS_1           2           145
  CLUS_2           2            12
  CLUS_3           7            20
  CLUS_4           0             3
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  22Q MUTATED        0      2      9      0      0
  22Q WILD-TYPE     46     42     52     14     20
D29V2, multiclass
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  22Q MUTATED        9      1      1
  22Q WILD-TYPE     61     51     43
D29V3, multiclass
        clus
vv       22Q MUTATED 22Q WILD-TYPE
  CLUS_1           9            61
  CLUS_2           1            51
  CLUS_3           1            43
D29V4, binary
               cls
clus              0   1
  22Q MUTATED     1  10
  22Q WILD-TYPE  55 100
[1] "tbl2"
               cls
clus            [,1] [,2]
  22Q MUTATED      1   10
  22Q WILD-TYPE   55  100
        clus
vv       22Q MUTATED 22Q WILD-TYPE
  CLUS_1           1            55
  CLUS_2          10           100
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  22Q MUTATED        0      5      2      4
  22Q WILD-TYPE     58     32     39     39
D29V5, multiclass
        clus
vv       22Q MUTATED 22Q WILD-TYPE
  CLUS_1           0            58
  CLUS_2           5            32
  CLUS_3           2            39
  CLUS_4           4            39
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  22Q MUTATED        5      2      4
  22Q WILD-TYPE     30     77     61
D29V6, multiclass
        clus
vv       22Q MUTATED 22Q WILD-TYPE
  CLUS_1           5            30
  CLUS_2           2            77
  CLUS_3           4            61

Clustering(30) Variable = XQ MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ MUTATED        0      1      5      2
  XQ WILD-TYPE    147     13     22      1
D30V1, multiclass
        clus
vv       XQ MUTATED XQ WILD-TYPE
  CLUS_1          0          147
  CLUS_2          1           13
  CLUS_3          5           22
  CLUS_4          2            1
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  XQ MUTATED        1      0      6      0      1
  XQ WILD-TYPE     45     44     55     14     19
D30V2, multiclass
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  XQ MUTATED        6      1      0
  XQ WILD-TYPE     64     51     44
D30V3, multiclass
        clus
vv       XQ MUTATED XQ WILD-TYPE
  CLUS_1          6           64
  CLUS_2          1           51
  CLUS_3          0           44
D30V4, binary
              cls
clus             0   1
  XQ MUTATED     1   6
  XQ WILD-TYPE  55 104
[1] "tbl2"
              cls
clus           [,1] [,2]
  XQ MUTATED      1    6
  XQ WILD-TYPE   55  104
        clus
vv       XQ MUTATED XQ WILD-TYPE
  CLUS_1          1           55
  CLUS_2          6          104
              vv
clus           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ MUTATED        1      5      1      1
  XQ WILD-TYPE     57     32     40     42
D30V5, multiclass
        clus
vv       XQ MUTATED XQ WILD-TYPE
  CLUS_1          1           57
  CLUS_2          5           32
  CLUS_3          1           40
  CLUS_4          1           42
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  XQ MUTATED        5      1      2
  XQ WILD-TYPE     30     78     63
D30V6, multiclass
        clus
vv       XQ MUTATED XQ WILD-TYPE
  CLUS_1          5           30
  CLUS_2          1           78
  CLUS_3          2           63
> q(save="no")
