
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/6159534/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/6159534/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 80 to 24."
[1] 24 28
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                4                24 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                4                24 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                5                23 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                5                23 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                6                22 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                6                22 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                3                25 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                3                25 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                8                20 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                8                20 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                7                21 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                7                21 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 25 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 25 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                 24 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                 24 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 8                 20 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 8                 20 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                 25 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                 25 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                 24 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                 24 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 4                 24 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 4                 24 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 4                 24 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 4                 24 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 5                 23 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 5                 23 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                 23 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                 23 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 6                 22 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 6                 22 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                3                25 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                3                25 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                25 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                25 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                3                25 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                3                25 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4                24 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4                24 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 5                 23 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 5                 23 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 24 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 24 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 3                 25 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 3                 25 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3                25 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3                25 
[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 = 1Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q GAIN MUTATED        0      2      2
  1Q GAIN WILD-TYPE      4     10     10
D1V1, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               2                10
  CLUS_3               2                10
D1V2, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    2  2
  1Q GAIN WILD-TYPE 13 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2    2
  1Q GAIN WILD-TYPE   13   11
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                13
  CLUS_2               2                11
D1V3, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    2  2
  1Q GAIN WILD-TYPE  8 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2    2
  1Q GAIN WILD-TYPE    8   16
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                 8
  CLUS_2               2                16

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

Clustering(3) Variable = 3Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q GAIN MUTATED        0      3      3
  3Q GAIN WILD-TYPE      4      9      9
D3V1, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               3                 9
  CLUS_3               3                 9
D3V2, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    3  3
  3Q GAIN WILD-TYPE 12 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3    3
  3Q GAIN WILD-TYPE   12   10
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                12
  CLUS_2               3                10
D3V3, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    3  3
  3Q GAIN WILD-TYPE  7 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3    3
  3Q GAIN WILD-TYPE    7   15
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                 7
  CLUS_2               3                15

Clustering(4) Variable = 6P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P GAIN MUTATED        0      2      1
  6P GAIN WILD-TYPE      4     10     11
D4V1, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               2                10
  CLUS_3               1                11
D4V2, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    2  1
  6P GAIN WILD-TYPE 13 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2    1
  6P GAIN WILD-TYPE   13   12
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2                13
  CLUS_2               1                12
D4V3, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    1  2
  6P GAIN WILD-TYPE  9 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      1    2
  6P GAIN WILD-TYPE    9   16
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1                 9
  CLUS_2               2                16

Clustering(5) Variable = 7P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P GAIN MUTATED        0      5      3
  7P GAIN WILD-TYPE      4      7      9
D5V1, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               5                 7
  CLUS_3               3                 9
D5V2, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    4  4
  7P GAIN WILD-TYPE 11  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4    4
  7P GAIN WILD-TYPE   11    9
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               4                11
  CLUS_2               4                 9
D5V3, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    4  4
  7P GAIN WILD-TYPE  6 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4    4
  7P GAIN WILD-TYPE    6   14
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               4                 6
  CLUS_2               4                14

Clustering(6) Variable = 7Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q GAIN MUTATED        0      4      3
  7Q GAIN WILD-TYPE      4      8      9
D6V1, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               4                 8
  CLUS_3               3                 9
D6V2, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    3  4
  7Q GAIN WILD-TYPE 12  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3    4
  7Q GAIN WILD-TYPE   12    9
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               3                12
  CLUS_2               4                 9
D6V3, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    4  3
  7Q GAIN WILD-TYPE  6 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      4    3
  7Q GAIN WILD-TYPE    6   15
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               4                 6
  CLUS_2               3                15

Clustering(7) Variable = 10P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P GAIN MUTATED        0      2      1
  10P GAIN WILD-TYPE      4     10     11
D7V1, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                2                 10
  CLUS_3                1                 11
D7V2, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    1  2
  10P GAIN WILD-TYPE 14 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1    2
  10P GAIN WILD-TYPE   14   11
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                2                 11
D7V3, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    1  2
  10P GAIN WILD-TYPE  9 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1    2
  10P GAIN WILD-TYPE    9   16
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                  9
  CLUS_2                2                 16

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

Clustering(9) Variable = 11Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q GAIN MUTATED        1      2      5
  11Q GAIN WILD-TYPE      3     10      7
D9V1, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                2                 10
  CLUS_3                5                  7
D9V2, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    5  3
  11Q GAIN WILD-TYPE 10 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      5    3
  11Q GAIN WILD-TYPE   10   10
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                5                 10
  CLUS_2                3                 10
D9V3, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    1  7
  11Q GAIN WILD-TYPE  9 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1    7
  11Q GAIN WILD-TYPE    9   11
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                  9
  CLUS_2                7                 11

Clustering(10) Variable = 12P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P GAIN MUTATED        0      1      2
  12P GAIN WILD-TYPE      4     11     10
D10V1, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                1                 11
  CLUS_3                2                 10
D10V2, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    1  2
  12P GAIN WILD-TYPE 14 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1    2
  12P GAIN WILD-TYPE   14   11
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                2                 11
D10V3, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    0  3
  12P GAIN WILD-TYPE 10 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0    3
  12P GAIN WILD-TYPE   10   15
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                0                 10
  CLUS_2                3                 15

Clustering(11) Variable = 12Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q GAIN MUTATED        0      1      3
  12Q GAIN WILD-TYPE      4     11      9
D11V1, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                1                 11
  CLUS_3                3                  9
D11V2, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    2  2
  12Q GAIN WILD-TYPE 13 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2    2
  12Q GAIN WILD-TYPE   13   11
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                 13
  CLUS_2                2                 11
D11V3, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    0  4
  12Q GAIN WILD-TYPE 10 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0    4
  12Q GAIN WILD-TYPE   10   14
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                0                 10
  CLUS_2                4                 14

Clustering(12) Variable = 16P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED        0      1      3
  16P GAIN WILD-TYPE      4     11      9
D12V1, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                1                 11
  CLUS_3                3                  9
D12V2, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    3  1
  16P GAIN WILD-TYPE 12 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3    1
  16P GAIN WILD-TYPE   12   12
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                3                 12
  CLUS_2                1                 12
D12V3, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    1  3
  16P GAIN WILD-TYPE  9 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1    3
  16P GAIN WILD-TYPE    9   15
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                  9
  CLUS_2                3                 15

Clustering(13) Variable = 16Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q GAIN MUTATED        0      0      4
  16Q GAIN WILD-TYPE      4     12      8
D13V1, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                0                 12
  CLUS_3                4                  8
D13V2, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    3  1
  16Q GAIN WILD-TYPE 12 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3    1
  16Q GAIN WILD-TYPE   12   12
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                3                 12
  CLUS_2                1                 12
D13V3, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    1  3
  16Q GAIN WILD-TYPE  9 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1    3
  16Q GAIN WILD-TYPE    9   15
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                  9
  CLUS_2                3                 15

Clustering(14) Variable = 18P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED        0      3      2
  18P GAIN WILD-TYPE      4      9     10
D14V1, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                3                  9
  CLUS_3                2                 10
D14V2, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    3  2
  18P GAIN WILD-TYPE 12 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3    2
  18P GAIN WILD-TYPE   12   11
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                3                 12
  CLUS_2                2                 11
D14V3, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    2  3
  18P GAIN WILD-TYPE  8 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2    3
  18P GAIN WILD-TYPE    8   15
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                2                  8
  CLUS_2                3                 15

Clustering(15) Variable = 18Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED        0      3      2
  18Q GAIN WILD-TYPE      4      9     10
D15V1, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                3                  9
  CLUS_3                2                 10
D15V2, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    3  2
  18Q GAIN WILD-TYPE 12 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3    2
  18Q GAIN WILD-TYPE   12   11
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                3                 12
  CLUS_2                2                 11
D15V3, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    2  3
  18Q GAIN WILD-TYPE  8 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2    3
  18Q GAIN WILD-TYPE    8   15
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                  8
  CLUS_2                3                 15

Clustering(16) Variable = 21Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED        1      2      3
  21Q GAIN WILD-TYPE      3     10      9
D16V1, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                2                 10
  CLUS_3                3                  9
D16V2, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    3  3
  21Q GAIN WILD-TYPE 12 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    3
  21Q GAIN WILD-TYPE   12   10
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                3                 12
  CLUS_2                3                 10
D16V3, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    2  4
  21Q GAIN WILD-TYPE  8 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2    4
  21Q GAIN WILD-TYPE    8   14
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                2                  8
  CLUS_2                4                 14

Clustering(17) Variable = XQ GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED        0      0      3
  XQ GAIN WILD-TYPE      4     12      9
D17V1, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                12
  CLUS_3               3                 9
D17V2, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    2  1
  XQ GAIN WILD-TYPE 13 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2    1
  XQ GAIN WILD-TYPE   13   12
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               2                13
  CLUS_2               1                12
D17V3, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    0  3
  XQ GAIN WILD-TYPE 10 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0    3
  XQ GAIN WILD-TYPE   10   15
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                10
  CLUS_2               3                15

Clustering(18) Variable = 1P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P LOSS MUTATED        0      2      1
  1P LOSS WILD-TYPE      4     10     11
D18V1, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               2                10
  CLUS_3               1                11
D18V2, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    2  1
  1P LOSS WILD-TYPE 13 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2    1
  1P LOSS WILD-TYPE   13   12
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               2                13
  CLUS_2               1                12
D18V3, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    1  2
  1P LOSS WILD-TYPE  9 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    2
  1P LOSS WILD-TYPE    9   16
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                 9
  CLUS_2               2                16

Clustering(19) Variable = 6Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q LOSS MUTATED        0      1      2
  6Q LOSS WILD-TYPE      4     11     10
D19V1, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               1                11
  CLUS_3               2                10
D19V2, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    2  1
  6Q LOSS WILD-TYPE 13 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      2    1
  6Q LOSS WILD-TYPE   13   12
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               2                13
  CLUS_2               1                12
D19V3, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    0  3
  6Q LOSS WILD-TYPE 10 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0    3
  6Q LOSS WILD-TYPE   10   15
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               0                10
  CLUS_2               3                15

Clustering(20) Variable = 8P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED        0      2      2
  8P LOSS WILD-TYPE      4     10     10
D20V1, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               2                10
  CLUS_3               2                10
D20V2, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    1  3
  8P LOSS WILD-TYPE 14 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1    3
  8P LOSS WILD-TYPE   14   10
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               1                14
  CLUS_2               3                10
D20V3, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    3  1
  8P LOSS WILD-TYPE  7 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      3    1
  8P LOSS WILD-TYPE    7   17
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               3                 7
  CLUS_2               1                17

Clustering(21) Variable = 15Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q LOSS MUTATED        0      4      1
  15Q LOSS WILD-TYPE      4      8     11
D21V1, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                4                  8
  CLUS_3                1                 11
D21V2, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    2  3
  15Q LOSS WILD-TYPE 13 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2    3
  15Q LOSS WILD-TYPE   13   10
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                2                 13
  CLUS_2                3                 10
D21V3, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    3  2
  15Q LOSS WILD-TYPE  7 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3    2
  15Q LOSS WILD-TYPE    7   16
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                3                  7
  CLUS_2                2                 16

Clustering(22) Variable = 16Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q LOSS MUTATED        0      2      2
  16Q LOSS WILD-TYPE      4     10     10
D22V1, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                2                 10
  CLUS_3                2                 10
D22V2, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    2  2
  16Q LOSS WILD-TYPE 13 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2    2
  16Q LOSS WILD-TYPE   13   11
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                2                 13
  CLUS_2                2                 11
D22V3, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    2  2
  16Q LOSS WILD-TYPE  8 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2    2
  16Q LOSS WILD-TYPE    8   16
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                2                  8
  CLUS_2                2                 16

Clustering(23) Variable = 17P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED        0      2      1
  17P LOSS WILD-TYPE      4     10     11
D23V1, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                2                 10
  CLUS_3                1                 11
D23V2, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    2  1
  17P LOSS WILD-TYPE 13 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      2    1
  17P LOSS WILD-TYPE   13   12
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                 13
  CLUS_2                1                 12
D23V3, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    1  2
  17P LOSS WILD-TYPE  9 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1    2
  17P LOSS WILD-TYPE    9   16
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                1                  9
  CLUS_2                2                 16

Clustering(24) Variable = XQ LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED        0      0      3
  XQ LOSS WILD-TYPE      4     12      9
D24V1, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                12
  CLUS_3               3                 9
D24V2, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    1  2
  XQ LOSS WILD-TYPE 14 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1    2
  XQ LOSS WILD-TYPE   14   11
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                14
  CLUS_2               2                11
D24V3, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    2  1
  XQ LOSS WILD-TYPE  8 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2    1
  XQ LOSS WILD-TYPE    8   17
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               2                 8
  CLUS_2               1                17
> q(save="no")
