
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/DLBC-TP/6159533/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/DLBC-TP/6159514/DLBC-TP.transferedmergedcluster.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ONLYSIG", "-oT=DLBC-TP", "-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=DLBC-TP"
[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/DLBC-TP/6159514/DLBC-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/DLBC-TP/6159533/transformed.cor.cli.txt"

nPatients in clinical file=28, in cluster file=28, common to both=28
[1] "Reduce the number of clustering variables from 40 to 29."
[1] 29 28
[1] "1P MUTATION ANALYSIS"
[1] 3
  1P MUTATED 1P WILD-TYPE 
           4           24 
  1P MUTATED 1P WILD-TYPE 
           4           24 
[1] "1Q MUTATION ANALYSIS"
[1] 3
  1Q MUTATED 1Q WILD-TYPE 
           5           23 
  1Q MUTATED 1Q WILD-TYPE 
           5           23 
[1] "2P MUTATION ANALYSIS"
[1] 3
  2P MUTATED 2P WILD-TYPE 
           4           24 
  2P MUTATED 2P WILD-TYPE 
           4           24 
[1] "2Q MUTATION ANALYSIS"
[1] 3
  2Q MUTATED 2Q WILD-TYPE 
           4           24 
  2Q MUTATED 2Q WILD-TYPE 
           4           24 
[1] "3P MUTATION ANALYSIS"
[1] 3
  3P MUTATED 3P WILD-TYPE 
           5           23 
  3P MUTATED 3P WILD-TYPE 
           5           23 
[1] "3Q MUTATION ANALYSIS"
[1] 3
  3Q MUTATED 3Q WILD-TYPE 
           6           22 
  3Q MUTATED 3Q WILD-TYPE 
           6           22 
[1] "6P MUTATION ANALYSIS"
[1] 3
  6P MUTATED 6P WILD-TYPE 
           4           24 
  6P MUTATED 6P WILD-TYPE 
           4           24 
[1] "6Q MUTATION ANALYSIS"
[1] 3
  6Q MUTATED 6Q WILD-TYPE 
           5           23 
  6Q MUTATED 6Q WILD-TYPE 
           5           23 
[1] "7P MUTATION ANALYSIS"
[1] 3
  7P MUTATED 7P WILD-TYPE 
           8           20 
  7P MUTATED 7P WILD-TYPE 
           8           20 
[1] "7Q MUTATION ANALYSIS"
[1] 3
  7Q MUTATED 7Q WILD-TYPE 
           7           21 
  7Q MUTATED 7Q WILD-TYPE 
           7           21 
[1] "8P MUTATION ANALYSIS"
[1] 3
  8P MUTATED 8P WILD-TYPE 
           6           22 
  8P MUTATED 8P WILD-TYPE 
           6           22 
[1] "8Q MUTATION ANALYSIS"
[1] 3
  8Q MUTATED 8Q WILD-TYPE 
           4           24 
  8Q MUTATED 8Q WILD-TYPE 
           4           24 
[1] "9P MUTATION ANALYSIS"
[1] 3
  9P MUTATED 9P WILD-TYPE 
           3           25 
  9P MUTATED 9P WILD-TYPE 
           3           25 
[1] "10P MUTATION ANALYSIS"
[1] 3
  10P MUTATED 10P WILD-TYPE 
            4            24 
  10P MUTATED 10P WILD-TYPE 
            4            24 
[1] "10Q MUTATION ANALYSIS"
[1] 3
  10Q MUTATED 10Q WILD-TYPE 
            3            25 
  10Q MUTATED 10Q WILD-TYPE 
            3            25 
[1] "11P MUTATION ANALYSIS"
[1] 3
  11P MUTATED 11P WILD-TYPE 
            4            24 
  11P MUTATED 11P WILD-TYPE 
            4            24 
[1] "11Q MUTATION ANALYSIS"
[1] 3
  11Q MUTATED 11Q WILD-TYPE 
            8            20 
  11Q MUTATED 11Q WILD-TYPE 
            8            20 
[1] "12P MUTATION ANALYSIS"
[1] 3
  12P MUTATED 12P WILD-TYPE 
            5            23 
  12P MUTATED 12P WILD-TYPE 
            5            23 
[1] "12Q MUTATION ANALYSIS"
[1] 3
  12Q MUTATED 12Q WILD-TYPE 
            5            23 
  12Q MUTATED 12Q WILD-TYPE 
            5            23 
[1] "13Q MUTATION ANALYSIS"
[1] 3
  13Q MUTATED 13Q WILD-TYPE 
            3            25 
  13Q MUTATED 13Q WILD-TYPE 
            3            25 
[1] "15Q MUTATION ANALYSIS"
[1] 3
  15Q MUTATED 15Q WILD-TYPE 
            6            22 
  15Q MUTATED 15Q WILD-TYPE 
            6            22 
[1] "16P MUTATION ANALYSIS"
[1] 3
  16P MUTATED 16P WILD-TYPE 
            6            22 
  16P MUTATED 16P WILD-TYPE 
            6            22 
[1] "16Q MUTATION ANALYSIS"
[1] 3
  16Q MUTATED 16Q WILD-TYPE 
            8            20 
  16Q MUTATED 16Q WILD-TYPE 
            8            20 
[1] "17P MUTATION ANALYSIS"
[1] 3
  17P MUTATED 17P WILD-TYPE 
            4            24 
  17P MUTATED 17P WILD-TYPE 
            4            24 
[1] "18P MUTATION ANALYSIS"
[1] 3
  18P MUTATED 18P WILD-TYPE 
            7            21 
  18P MUTATED 18P WILD-TYPE 
            7            21 
[1] "18Q MUTATION ANALYSIS"
[1] 3
  18Q MUTATED 18Q WILD-TYPE 
            7            21 
  18Q MUTATED 18Q WILD-TYPE 
            7            21 
[1] "20P MUTATION ANALYSIS"
[1] 3
  20P MUTATED 20P WILD-TYPE 
            3            25 
  20P MUTATED 20P WILD-TYPE 
            3            25 
[1] "21Q MUTATION ANALYSIS"
[1] 3
  21Q MUTATED 21Q WILD-TYPE 
            7            21 
  21Q MUTATED 21Q WILD-TYPE 
            7            21 
[1] "XQ MUTATION ANALYSIS"
[1] 3
  XQ MUTATED XQ WILD-TYPE 
           6           22 
  XQ MUTATED XQ WILD-TYPE 
           6           22 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
[1] "METHLYATION_CNMF"      "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL"

Input Data has 3 rows and 28 columns.

Variable 1:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNASEQ_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "METHLYATION_CNMF"      "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 28 columns, 0 survival variables, and 3 non-survival variables.
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=2, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  1P MUTATED        0      3      1
  1P WILD-TYPE      4      9     11
D1V1, multiclass
        clus
vv       1P MUTATED 1P WILD-TYPE
  CLUS_1          0            4
  CLUS_2          3            9
  CLUS_3          1           11
D1V2, binary
              cls
clus            0  1
  1P MUTATED    2  2
  1P WILD-TYPE 13 11
[1] "tbl2"
              cls
clus           [,1] [,2]
  1P MUTATED      2    2
  1P WILD-TYPE   13   11
        clus
vv       1P MUTATED 1P WILD-TYPE
  CLUS_1          2           13
  CLUS_2          2           11
D1V3, binary
              cls
clus            0  1
  1P MUTATED    2  2
  1P WILD-TYPE  8 16
[1] "tbl2"
              cls
clus           [,1] [,2]
  1P MUTATED      2    2
  1P WILD-TYPE    8   16
        clus
vv       1P MUTATED 1P WILD-TYPE
  CLUS_1          2            8
  CLUS_2          2           16

Clustering(2) Variable = 1Q MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  1Q MUTATED        0      2      3
  1Q WILD-TYPE      4     10      9
D2V1, multiclass
        clus
vv       1Q MUTATED 1Q WILD-TYPE
  CLUS_1          0            4
  CLUS_2          2           10
  CLUS_3          3            9
D2V2, binary
              cls
clus            0  1
  1Q MUTATED    3  2
  1Q WILD-TYPE 12 11
[1] "tbl2"
              cls
clus           [,1] [,2]
  1Q MUTATED      3    2
  1Q WILD-TYPE   12   11
        clus
vv       1Q MUTATED 1Q WILD-TYPE
  CLUS_1          3           12
  CLUS_2          2           11
D2V3, binary
              cls
clus            0  1
  1Q MUTATED    2  3
  1Q WILD-TYPE  8 15
[1] "tbl2"
              cls
clus           [,1] [,2]
  1Q MUTATED      2    3
  1Q WILD-TYPE    8   15
        clus
vv       1Q MUTATED 1Q WILD-TYPE
  CLUS_1          2            8
  CLUS_2          3           15

Clustering(3) Variable = 2P MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  2P MUTATED        0      1      3
  2P WILD-TYPE      4     11      9
D3V1, multiclass
        clus
vv       2P MUTATED 2P WILD-TYPE
  CLUS_1          0            4
  CLUS_2          1           11
  CLUS_3          3            9
D3V2, binary
              cls
clus            0  1
  2P MUTATED    2  2
  2P WILD-TYPE 13 11
[1] "tbl2"
              cls
clus           [,1] [,2]
  2P MUTATED      2    2
  2P WILD-TYPE   13   11
        clus
vv       2P MUTATED 2P WILD-TYPE
  CLUS_1          2           13
  CLUS_2          2           11
D3V3, binary
              cls
clus            0  1
  2P MUTATED    1  3
  2P WILD-TYPE  9 15
[1] "tbl2"
              cls
clus           [,1] [,2]
  2P MUTATED      1    3
  2P WILD-TYPE    9   15
        clus
vv       2P MUTATED 2P WILD-TYPE
  CLUS_1          1            9
  CLUS_2          3           15

Clustering(4) Variable = 2Q MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  2Q MUTATED        0      1      3
  2Q WILD-TYPE      4     11      9
D4V1, multiclass
        clus
vv       2Q MUTATED 2Q WILD-TYPE
  CLUS_1          0            4
  CLUS_2          1           11
  CLUS_3          3            9
D4V2, binary
              cls
clus            0  1
  2Q MUTATED    2  2
  2Q WILD-TYPE 13 11
[1] "tbl2"
              cls
clus           [,1] [,2]
  2Q MUTATED      2    2
  2Q WILD-TYPE   13   11
        clus
vv       2Q MUTATED 2Q WILD-TYPE
  CLUS_1          2           13
  CLUS_2          2           11
D4V3, binary
              cls
clus            0  1
  2Q MUTATED    1  3
  2Q WILD-TYPE  9 15
[1] "tbl2"
              cls
clus           [,1] [,2]
  2Q MUTATED      1    3
  2Q WILD-TYPE    9   15
        clus
vv       2Q MUTATED 2Q WILD-TYPE
  CLUS_1          1            9
  CLUS_2          3           15

Clustering(5) Variable = 3P MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  3P MUTATED        0      3      2
  3P WILD-TYPE      4      9     10
D5V1, multiclass
        clus
vv       3P MUTATED 3P WILD-TYPE
  CLUS_1          0            4
  CLUS_2          3            9
  CLUS_3          2           10
D5V2, binary
              cls
clus            0  1
  3P MUTATED    3  2
  3P WILD-TYPE 12 11
[1] "tbl2"
              cls
clus           [,1] [,2]
  3P MUTATED      3    2
  3P WILD-TYPE   12   11
        clus
vv       3P MUTATED 3P WILD-TYPE
  CLUS_1          3           12
  CLUS_2          2           11
D5V3, binary
              cls
clus            0  1
  3P MUTATED    2  3
  3P WILD-TYPE  8 15
[1] "tbl2"
              cls
clus           [,1] [,2]
  3P MUTATED      2    3
  3P WILD-TYPE    8   15
        clus
vv       3P MUTATED 3P WILD-TYPE
  CLUS_1          2            8
  CLUS_2          3           15

Clustering(6) Variable = 3Q MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  3Q MUTATED        0      3      3
  3Q WILD-TYPE      4      9      9
D6V1, multiclass
        clus
vv       3Q MUTATED 3Q WILD-TYPE
  CLUS_1          0            4
  CLUS_2          3            9
  CLUS_3          3            9
D6V2, binary
              cls
clus            0  1
  3Q MUTATED    3  3
  3Q WILD-TYPE 12 10
[1] "tbl2"
              cls
clus           [,1] [,2]
  3Q MUTATED      3    3
  3Q WILD-TYPE   12   10
        clus
vv       3Q MUTATED 3Q WILD-TYPE
  CLUS_1          3           12
  CLUS_2          3           10
D6V3, binary
              cls
clus            0  1
  3Q MUTATED    3  3
  3Q WILD-TYPE  7 15
[1] "tbl2"
              cls
clus           [,1] [,2]
  3Q MUTATED      3    3
  3Q WILD-TYPE    7   15
        clus
vv       3Q MUTATED 3Q WILD-TYPE
  CLUS_1          3            7
  CLUS_2          3           15

Clustering(7) Variable = 6P MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  6P MUTATED        0      3      1
  6P WILD-TYPE      4      9     11
D7V1, multiclass
        clus
vv       6P MUTATED 6P WILD-TYPE
  CLUS_1          0            4
  CLUS_2          3            9
  CLUS_3          1           11
D7V2, binary
              cls
clus            0  1
  6P MUTATED    2  2
  6P WILD-TYPE 13 11
[1] "tbl2"
              cls
clus           [,1] [,2]
  6P MUTATED      2    2
  6P WILD-TYPE   13   11
        clus
vv       6P MUTATED 6P WILD-TYPE
  CLUS_1          2           13
  CLUS_2          2           11
D7V3, binary
              cls
clus            0  1
  6P MUTATED    1  3
  6P WILD-TYPE  9 15
[1] "tbl2"
              cls
clus           [,1] [,2]
  6P MUTATED      1    3
  6P WILD-TYPE    9   15
        clus
vv       6P MUTATED 6P WILD-TYPE
  CLUS_1          1            9
  CLUS_2          3           15

Clustering(8) Variable = 6Q MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  6Q MUTATED        0      2      3
  6Q WILD-TYPE      4     10      9
D8V1, multiclass
        clus
vv       6Q MUTATED 6Q WILD-TYPE
  CLUS_1          0            4
  CLUS_2          2           10
  CLUS_3          3            9
D8V2, binary
              cls
clus            0  1
  6Q MUTATED    3  2
  6Q WILD-TYPE 12 11
[1] "tbl2"
              cls
clus           [,1] [,2]
  6Q MUTATED      3    2
  6Q WILD-TYPE   12   11
        clus
vv       6Q MUTATED 6Q WILD-TYPE
  CLUS_1          3           12
  CLUS_2          2           11
D8V3, binary
              cls
clus            0  1
  6Q MUTATED    1  4
  6Q WILD-TYPE  9 14
[1] "tbl2"
              cls
clus           [,1] [,2]
  6Q MUTATED      1    4
  6Q WILD-TYPE    9   14
        clus
vv       6Q MUTATED 6Q WILD-TYPE
  CLUS_1          1            9
  CLUS_2          4           14

Clustering(9) Variable = 7P MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  7P MUTATED        0      5      3
  7P WILD-TYPE      4      7      9
D9V1, multiclass
        clus
vv       7P MUTATED 7P WILD-TYPE
  CLUS_1          0            4
  CLUS_2          5            7
  CLUS_3          3            9
D9V2, binary
              cls
clus            0  1
  7P MUTATED    4  4
  7P WILD-TYPE 11  9
[1] "tbl2"
              cls
clus           [,1] [,2]
  7P MUTATED      4    4
  7P WILD-TYPE   11    9
        clus
vv       7P MUTATED 7P WILD-TYPE
  CLUS_1          4           11
  CLUS_2          4            9
D9V3, binary
              cls
clus            0  1
  7P MUTATED    4  4
  7P WILD-TYPE  6 14
[1] "tbl2"
              cls
clus           [,1] [,2]
  7P MUTATED      4    4
  7P WILD-TYPE    6   14
        clus
vv       7P MUTATED 7P WILD-TYPE
  CLUS_1          4            6
  CLUS_2          4           14

Clustering(10) Variable = 7Q MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  7Q MUTATED        0      4      3
  7Q WILD-TYPE      4      8      9
D10V1, multiclass
        clus
vv       7Q MUTATED 7Q WILD-TYPE
  CLUS_1          0            4
  CLUS_2          4            8
  CLUS_3          3            9
D10V2, binary
              cls
clus            0  1
  7Q MUTATED    3  4
  7Q WILD-TYPE 12  9
[1] "tbl2"
              cls
clus           [,1] [,2]
  7Q MUTATED      3    4
  7Q WILD-TYPE   12    9
        clus
vv       7Q MUTATED 7Q WILD-TYPE
  CLUS_1          3           12
  CLUS_2          4            9
D10V3, binary
              cls
clus            0  1
  7Q MUTATED    4  3
  7Q WILD-TYPE  6 15
[1] "tbl2"
              cls
clus           [,1] [,2]
  7Q MUTATED      4    3
  7Q WILD-TYPE    6   15
        clus
vv       7Q MUTATED 7Q WILD-TYPE
  CLUS_1          4            6
  CLUS_2          3           15

Clustering(11) Variable = 8P MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  8P MUTATED        0      3      3
  8P WILD-TYPE      4      9      9
D11V1, multiclass
        clus
vv       8P MUTATED 8P WILD-TYPE
  CLUS_1          0            4
  CLUS_2          3            9
  CLUS_3          3            9
D11V2, binary
              cls
clus            0  1
  8P MUTATED    1  5
  8P WILD-TYPE 14  8
[1] "tbl2"
              cls
clus           [,1] [,2]
  8P MUTATED      1    5
  8P WILD-TYPE   14    8
        clus
vv       8P MUTATED 8P WILD-TYPE
  CLUS_1          1           14
  CLUS_2          5            8
D11V3, binary
              cls
clus            0  1
  8P MUTATED    4  2
  8P WILD-TYPE  6 16
[1] "tbl2"
              cls
clus           [,1] [,2]
  8P MUTATED      4    2
  8P WILD-TYPE    6   16
        clus
vv       8P MUTATED 8P WILD-TYPE
  CLUS_1          4            6
  CLUS_2          2           16

Clustering(12) Variable = 8Q MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  8Q MUTATED        0      2      2
  8Q WILD-TYPE      4     10     10
D12V1, multiclass
        clus
vv       8Q MUTATED 8Q WILD-TYPE
  CLUS_1          0            4
  CLUS_2          2           10
  CLUS_3          2           10
D12V2, binary
              cls
clus            0  1
  8Q MUTATED    1  3
  8Q WILD-TYPE 14 10
[1] "tbl2"
              cls
clus           [,1] [,2]
  8Q MUTATED      1    3
  8Q WILD-TYPE   14   10
        clus
vv       8Q MUTATED 8Q WILD-TYPE
  CLUS_1          1           14
  CLUS_2          3           10
D12V3, binary
              cls
clus            0  1
  8Q MUTATED    2  2
  8Q WILD-TYPE  8 16
[1] "tbl2"
              cls
clus           [,1] [,2]
  8Q MUTATED      2    2
  8Q WILD-TYPE    8   16
        clus
vv       8Q MUTATED 8Q WILD-TYPE
  CLUS_1          2            8
  CLUS_2          2           16

Clustering(13) Variable = 9P MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  9P MUTATED        0      1      2
  9P WILD-TYPE      4     11     10
D13V1, multiclass
        clus
vv       9P MUTATED 9P WILD-TYPE
  CLUS_1          0            4
  CLUS_2          1           11
  CLUS_3          2           10
D13V2, binary
              cls
clus            0  1
  9P MUTATED    2  1
  9P WILD-TYPE 13 12
[1] "tbl2"
              cls
clus           [,1] [,2]
  9P MUTATED      2    1
  9P WILD-TYPE   13   12
        clus
vv       9P MUTATED 9P WILD-TYPE
  CLUS_1          2           13
  CLUS_2          1           12
D13V3, binary
              cls
clus            0  1
  9P MUTATED    0  3
  9P WILD-TYPE 10 15
[1] "tbl2"
              cls
clus           [,1] [,2]
  9P MUTATED      0    3
  9P WILD-TYPE   10   15
        clus
vv       9P MUTATED 9P WILD-TYPE
  CLUS_1          0           10
  CLUS_2          3           15

Clustering(14) Variable = 10P MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  10P MUTATED        0      3      1
  10P WILD-TYPE      4      9     11
D14V1, multiclass
        clus
vv       10P MUTATED 10P WILD-TYPE
  CLUS_1           0             4
  CLUS_2           3             9
  CLUS_3           1            11
D14V2, binary
               cls
clus             0  1
  10P MUTATED    1  3
  10P WILD-TYPE 14 10
[1] "tbl2"
               cls
clus            [,1] [,2]
  10P MUTATED      1    3
  10P WILD-TYPE   14   10
        clus
vv       10P MUTATED 10P WILD-TYPE
  CLUS_1           1            14
  CLUS_2           3            10
D14V3, binary
               cls
clus             0  1
  10P MUTATED    2  2
  10P WILD-TYPE  8 16
[1] "tbl2"
               cls
clus            [,1] [,2]
  10P MUTATED      2    2
  10P WILD-TYPE    8   16
        clus
vv       10P MUTATED 10P WILD-TYPE
  CLUS_1           2             8
  CLUS_2           2            16

Clustering(15) Variable = 10Q MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  10Q MUTATED        0      2      1
  10Q WILD-TYPE      4     10     11
D15V1, multiclass
        clus
vv       10Q MUTATED 10Q WILD-TYPE
  CLUS_1           0             4
  CLUS_2           2            10
  CLUS_3           1            11
D15V2, binary
               cls
clus             0  1
  10Q MUTATED    0  3
  10Q WILD-TYPE 15 10
[1] "tbl2"
               cls
clus            [,1] [,2]
  10Q MUTATED      0    3
  10Q WILD-TYPE   15   10
        clus
vv       10Q MUTATED 10Q WILD-TYPE
  CLUS_1           0            15
  CLUS_2           3            10
D15V3, binary
               cls
clus             0  1
  10Q MUTATED    2  1
  10Q WILD-TYPE  8 17
[1] "tbl2"
               cls
clus            [,1] [,2]
  10Q MUTATED      2    1
  10Q WILD-TYPE    8   17
        clus
vv       10Q MUTATED 10Q WILD-TYPE
  CLUS_1           2             8
  CLUS_2           1            17

Clustering(16) Variable = 11P MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  11P MUTATED        0      1      3
  11P WILD-TYPE      4     11      9
D16V1, multiclass
        clus
vv       11P MUTATED 11P WILD-TYPE
  CLUS_1           0             4
  CLUS_2           1            11
  CLUS_3           3             9
D16V2, binary
               cls
clus             0  1
  11P MUTATED    3  1
  11P WILD-TYPE 12 12
[1] "tbl2"
               cls
clus            [,1] [,2]
  11P MUTATED      3    1
  11P WILD-TYPE   12   12
        clus
vv       11P MUTATED 11P WILD-TYPE
  CLUS_1           3            12
  CLUS_2           1            12
D16V3, binary
               cls
clus             0  1
  11P MUTATED    0  4
  11P WILD-TYPE 10 14
[1] "tbl2"
               cls
clus            [,1] [,2]
  11P MUTATED      0    4
  11P WILD-TYPE   10   14
        clus
vv       11P MUTATED 11P WILD-TYPE
  CLUS_1           0            10
  CLUS_2           4            14

Clustering(17) Variable = 11Q MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  11Q MUTATED        1      2      5
  11Q WILD-TYPE      3     10      7
D17V1, multiclass
        clus
vv       11Q MUTATED 11Q WILD-TYPE
  CLUS_1           1             3
  CLUS_2           2            10
  CLUS_3           5             7
D17V2, binary
               cls
clus             0  1
  11Q MUTATED    5  3
  11Q WILD-TYPE 10 10
[1] "tbl2"
               cls
clus            [,1] [,2]
  11Q MUTATED      5    3
  11Q WILD-TYPE   10   10
        clus
vv       11Q MUTATED 11Q WILD-TYPE
  CLUS_1           5            10
  CLUS_2           3            10
D17V3, binary
               cls
clus             0  1
  11Q MUTATED    1  7
  11Q WILD-TYPE  9 11
[1] "tbl2"
               cls
clus            [,1] [,2]
  11Q MUTATED      1    7
  11Q WILD-TYPE    9   11
        clus
vv       11Q MUTATED 11Q WILD-TYPE
  CLUS_1           1             9
  CLUS_2           7            11

Clustering(18) Variable = 12P MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  12P MUTATED        0      3      2
  12P WILD-TYPE      4      9     10
D18V1, multiclass
        clus
vv       12P MUTATED 12P WILD-TYPE
  CLUS_1           0             4
  CLUS_2           3             9
  CLUS_3           2            10
D18V2, binary
               cls
clus             0  1
  12P MUTATED    2  3
  12P WILD-TYPE 13 10
[1] "tbl2"
               cls
clus            [,1] [,2]
  12P MUTATED      2    3
  12P WILD-TYPE   13   10
        clus
vv       12P MUTATED 12P WILD-TYPE
  CLUS_1           2            13
  CLUS_2           3            10
D18V3, binary
               cls
clus             0  1
  12P MUTATED    1  4
  12P WILD-TYPE  9 14
[1] "tbl2"
               cls
clus            [,1] [,2]
  12P MUTATED      1    4
  12P WILD-TYPE    9   14
        clus
vv       12P MUTATED 12P WILD-TYPE
  CLUS_1           1             9
  CLUS_2           4            14

Clustering(19) Variable = 12Q MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  12Q MUTATED        0      2      3
  12Q WILD-TYPE      4     10      9
D19V1, multiclass
        clus
vv       12Q MUTATED 12Q WILD-TYPE
  CLUS_1           0             4
  CLUS_2           2            10
  CLUS_3           3             9
D19V2, binary
               cls
clus             0  1
  12Q MUTATED    2  3
  12Q WILD-TYPE 13 10
[1] "tbl2"
               cls
clus            [,1] [,2]
  12Q MUTATED      2    3
  12Q WILD-TYPE   13   10
        clus
vv       12Q MUTATED 12Q WILD-TYPE
  CLUS_1           2            13
  CLUS_2           3            10
D19V3, binary
               cls
clus             0  1
  12Q MUTATED    1  4
  12Q WILD-TYPE  9 14
[1] "tbl2"
               cls
clus            [,1] [,2]
  12Q MUTATED      1    4
  12Q WILD-TYPE    9   14
        clus
vv       12Q MUTATED 12Q WILD-TYPE
  CLUS_1           1             9
  CLUS_2           4            14

Clustering(20) Variable = 13Q MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  13Q MUTATED        0      3      0
  13Q WILD-TYPE      4      9     12
D20V1, multiclass
        clus
vv       13Q MUTATED 13Q WILD-TYPE
  CLUS_1           0             4
  CLUS_2           3             9
  CLUS_3           0            12
D20V2, binary
               cls
clus             0  1
  13Q MUTATED    1  2
  13Q WILD-TYPE 14 11
[1] "tbl2"
               cls
clus            [,1] [,2]
  13Q MUTATED      1    2
  13Q WILD-TYPE   14   11
        clus
vv       13Q MUTATED 13Q WILD-TYPE
  CLUS_1           1            14
  CLUS_2           2            11
D20V3, binary
               cls
clus             0  1
  13Q MUTATED    2  1
  13Q WILD-TYPE  8 17
[1] "tbl2"
               cls
clus            [,1] [,2]
  13Q MUTATED      2    1
  13Q WILD-TYPE    8   17
        clus
vv       13Q MUTATED 13Q WILD-TYPE
  CLUS_1           2             8
  CLUS_2           1            17

Clustering(21) Variable = 15Q MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  15Q MUTATED        0      5      1
  15Q WILD-TYPE      4      7     11
D21V1, multiclass
        clus
vv       15Q MUTATED 15Q WILD-TYPE
  CLUS_1           0             4
  CLUS_2           5             7
  CLUS_3           1            11
D21V2, binary
               cls
clus             0  1
  15Q MUTATED    2  4
  15Q WILD-TYPE 13  9
[1] "tbl2"
               cls
clus            [,1] [,2]
  15Q MUTATED      2    4
  15Q WILD-TYPE   13    9
        clus
vv       15Q MUTATED 15Q WILD-TYPE
  CLUS_1           2            13
  CLUS_2           4             9
D21V3, binary
               cls
clus             0  1
  15Q MUTATED    4  2
  15Q WILD-TYPE  6 16
[1] "tbl2"
               cls
clus            [,1] [,2]
  15Q MUTATED      4    2
  15Q WILD-TYPE    6   16
        clus
vv       15Q MUTATED 15Q WILD-TYPE
  CLUS_1           4             6
  CLUS_2           2            16

Clustering(22) Variable = 16P MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  16P MUTATED        0      2      4
  16P WILD-TYPE      4     10      8
D22V1, multiclass
        clus
vv       16P MUTATED 16P WILD-TYPE
  CLUS_1           0             4
  CLUS_2           2            10
  CLUS_3           4             8
D22V2, binary
               cls
clus             0  1
  16P MUTATED    4  2
  16P WILD-TYPE 11 11
[1] "tbl2"
               cls
clus            [,1] [,2]
  16P MUTATED      4    2
  16P WILD-TYPE   11   11
        clus
vv       16P MUTATED 16P WILD-TYPE
  CLUS_1           4            11
  CLUS_2           2            11
D22V3, binary
               cls
clus             0  1
  16P MUTATED    2  4
  16P WILD-TYPE  8 14
[1] "tbl2"
               cls
clus            [,1] [,2]
  16P MUTATED      2    4
  16P WILD-TYPE    8   14
        clus
vv       16P MUTATED 16P WILD-TYPE
  CLUS_1           2             8
  CLUS_2           4            14

Clustering(23) Variable = 16Q MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  16Q MUTATED        0      2      6
  16Q WILD-TYPE      4     10      6
D23V1, multiclass
        clus
vv       16Q MUTATED 16Q WILD-TYPE
  CLUS_1           0             4
  CLUS_2           2            10
  CLUS_3           6             6
D23V2, binary
               cls
clus             0  1
  16Q MUTATED    5  3
  16Q WILD-TYPE 10 10
[1] "tbl2"
               cls
clus            [,1] [,2]
  16Q MUTATED      5    3
  16Q WILD-TYPE   10   10
        clus
vv       16Q MUTATED 16Q WILD-TYPE
  CLUS_1           5            10
  CLUS_2           3            10
D23V3, binary
               cls
clus             0  1
  16Q MUTATED    3  5
  16Q WILD-TYPE  7 13
[1] "tbl2"
               cls
clus            [,1] [,2]
  16Q MUTATED      3    5
  16Q WILD-TYPE    7   13
        clus
vv       16Q MUTATED 16Q WILD-TYPE
  CLUS_1           3             7
  CLUS_2           5            13

Clustering(24) Variable = 17P MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  17P MUTATED        0      2      2
  17P WILD-TYPE      4     10     10
D24V1, multiclass
        clus
vv       17P MUTATED 17P WILD-TYPE
  CLUS_1           0             4
  CLUS_2           2            10
  CLUS_3           2            10
D24V2, binary
               cls
clus             0  1
  17P MUTATED    2  2
  17P WILD-TYPE 13 11
[1] "tbl2"
               cls
clus            [,1] [,2]
  17P MUTATED      2    2
  17P WILD-TYPE   13   11
        clus
vv       17P MUTATED 17P WILD-TYPE
  CLUS_1           2            13
  CLUS_2           2            11
D24V3, binary
               cls
clus             0  1
  17P MUTATED    1  3
  17P WILD-TYPE  9 15
[1] "tbl2"
               cls
clus            [,1] [,2]
  17P MUTATED      1    3
  17P WILD-TYPE    9   15
        clus
vv       17P MUTATED 17P WILD-TYPE
  CLUS_1           1             9
  CLUS_2           3            15

Clustering(25) Variable = 18P MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  18P MUTATED        0      4      3
  18P WILD-TYPE      4      8      9
D25V1, multiclass
        clus
vv       18P MUTATED 18P WILD-TYPE
  CLUS_1           0             4
  CLUS_2           4             8
  CLUS_3           3             9
D25V2, binary
               cls
clus             0  1
  18P MUTATED    5  2
  18P WILD-TYPE 10 11
[1] "tbl2"
               cls
clus            [,1] [,2]
  18P MUTATED      5    2
  18P WILD-TYPE   10   11
        clus
vv       18P MUTATED 18P WILD-TYPE
  CLUS_1           5            10
  CLUS_2           2            11
D25V3, binary
               cls
clus             0  1
  18P MUTATED    2  5
  18P WILD-TYPE  8 13
[1] "tbl2"
               cls
clus            [,1] [,2]
  18P MUTATED      2    5
  18P WILD-TYPE    8   13
        clus
vv       18P MUTATED 18P WILD-TYPE
  CLUS_1           2             8
  CLUS_2           5            13

Clustering(26) Variable = 18Q MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  18Q MUTATED        0      4      3
  18Q WILD-TYPE      4      8      9
D26V1, multiclass
        clus
vv       18Q MUTATED 18Q WILD-TYPE
  CLUS_1           0             4
  CLUS_2           4             8
  CLUS_3           3             9
D26V2, binary
               cls
clus             0  1
  18Q MUTATED    5  2
  18Q WILD-TYPE 10 11
[1] "tbl2"
               cls
clus            [,1] [,2]
  18Q MUTATED      5    2
  18Q WILD-TYPE   10   11
        clus
vv       18Q MUTATED 18Q WILD-TYPE
  CLUS_1           5            10
  CLUS_2           2            11
D26V3, binary
               cls
clus             0  1
  18Q MUTATED    2  5
  18Q WILD-TYPE  8 13
[1] "tbl2"
               cls
clus            [,1] [,2]
  18Q MUTATED      2    5
  18Q WILD-TYPE    8   13
        clus
vv       18Q MUTATED 18Q WILD-TYPE
  CLUS_1           2             8
  CLUS_2           5            13

Clustering(27) Variable = 20P MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  20P MUTATED        0      1      2
  20P WILD-TYPE      4     11     10
D27V1, multiclass
        clus
vv       20P MUTATED 20P WILD-TYPE
  CLUS_1           0             4
  CLUS_2           1            11
  CLUS_3           2            10
D27V2, binary
               cls
clus             0  1
  20P MUTATED    1  2
  20P WILD-TYPE 14 11
[1] "tbl2"
               cls
clus            [,1] [,2]
  20P MUTATED      1    2
  20P WILD-TYPE   14   11
        clus
vv       20P MUTATED 20P WILD-TYPE
  CLUS_1           1            14
  CLUS_2           2            11
D27V3, binary
               cls
clus             0  1
  20P MUTATED    1  2
  20P WILD-TYPE  9 16
[1] "tbl2"
               cls
clus            [,1] [,2]
  20P MUTATED      1    2
  20P WILD-TYPE    9   16
        clus
vv       20P MUTATED 20P WILD-TYPE
  CLUS_1           1             9
  CLUS_2           2            16

Clustering(28) Variable = 21Q MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  21Q MUTATED        1      3      3
  21Q WILD-TYPE      3      9      9
D28V1, multiclass
        clus
vv       21Q MUTATED 21Q WILD-TYPE
  CLUS_1           1             3
  CLUS_2           3             9
  CLUS_3           3             9
D28V2, binary
               cls
clus             0  1
  21Q MUTATED    3  4
  21Q WILD-TYPE 12  9
[1] "tbl2"
               cls
clus            [,1] [,2]
  21Q MUTATED      3    4
  21Q WILD-TYPE   12    9
        clus
vv       21Q MUTATED 21Q WILD-TYPE
  CLUS_1           3            12
  CLUS_2           4             9
D28V3, binary
               cls
clus             0  1
  21Q MUTATED    3  4
  21Q WILD-TYPE  7 14
[1] "tbl2"
               cls
clus            [,1] [,2]
  21Q MUTATED      3    4
  21Q WILD-TYPE    7   14
        clus
vv       21Q MUTATED 21Q WILD-TYPE
  CLUS_1           3             7
  CLUS_2           4            14

Clustering(29) Variable = XQ MUTATION ANALYSIS
              vv
clus           CLUS_1 CLUS_2 CLUS_3
  XQ MUTATED        0      0      6
  XQ WILD-TYPE      4     12      6
D29V1, multiclass
        clus
vv       XQ MUTATED XQ WILD-TYPE
  CLUS_1          0            4
  CLUS_2          0           12
  CLUS_3          6            6
D29V2, binary
              cls
clus            0  1
  XQ MUTATED    3  3
  XQ WILD-TYPE 12 10
[1] "tbl2"
              cls
clus           [,1] [,2]
  XQ MUTATED      3    3
  XQ WILD-TYPE   12   10
        clus
vv       XQ MUTATED XQ WILD-TYPE
  CLUS_1          3           12
  CLUS_2          3           10
D29V3, binary
              cls
clus            0  1
  XQ MUTATED    2  4
  XQ WILD-TYPE  8 14
[1] "tbl2"
              cls
clus           [,1] [,2]
  XQ MUTATED      2    4
  XQ WILD-TYPE    8   14
        clus
vv       XQ MUTATED XQ WILD-TYPE
  CLUS_1          2            8
  CLUS_2          4           14
> q(save="no")
