
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_cnvarms_onlysig.2.4053/CNV2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_cnvarms_onlysig.2.4053/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/375831/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/ESCA-TP/2907363/1.GDAC_mergedClustering.Finished/ESCA-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=ESCA-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=ESCA-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=50, in cluster file=20, common to both=20
[1] "Reduce the number of clustering variables from 80 to 38."
[1] 38 20
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                4                16 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                4                16 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                3                17 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                3                17 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                16 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                16 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                7                13 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                7                13 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                6                14 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                6                14 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                7                13 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                7                13 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                6                14 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                6                14 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                7                13 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                7                13 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               11                 9 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               11                 9 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4                16 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4                16 
[1] "10p gain mutation analysis"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                 16 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                 16 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 9                 11 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 9                 11 
[1] "14q gain mutation analysis"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                 16 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                 16 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 5                 15 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 5                 15 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 5                 15 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 5                 15 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 4                 16 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 4                 16 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                10                 10 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                10                 10 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                10                 10 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                10                 10 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                 17 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                 17 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                 15 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                 15 
[1] "Xq gain mutation analysis"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4                16 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4                16 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                7                13 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                7                13 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                6                14 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                6                14 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                5                15 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                5                15 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                16 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                16 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                4                16 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                4                16 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                6                14 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                6                14 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                3                17 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                3                17 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                3                17 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                3                17 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 4                 16 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 4                 16 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 3                 17 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 3                 17 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 3                 17 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 3                 17 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 7                 13 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 7                 13 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 16 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 16 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 6                 14 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 6                 14 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 7                 13 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 7                 13 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                10                 10 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                10                 10 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 3                 17 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 3                 17 
[1] "data2feature, selection=ALL"
[1] "METHLYATION_CNMF"

Input Data has 1 rows and 20 columns.

Variable 1:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "METHLYATION_CNMF"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 20 columns, 0 survival variables, and 1 non-survival variables.
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1q gain mutation analysis
D1V1, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                10
  CLUS_2               2                 3
  CLUS_3               0                 3

Clustering(2) Variable = 2p gain mutation analysis
D2V1, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               3                 9
  CLUS_2               0                 5
  CLUS_3               0                 3

Clustering(3) Variable = 3p gain mutation analysis
D3V1, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3                 9
  CLUS_2               1                 4
  CLUS_3               0                 3

Clustering(4) Variable = 3q gain mutation analysis
D4V1, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               6                 6
  CLUS_2               1                 4
  CLUS_3               0                 3

Clustering(5) Variable = 5p gain mutation analysis
D5V1, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               4                 8
  CLUS_2               1                 4
  CLUS_3               1                 2

Clustering(6) Variable = 7p gain mutation analysis
D6V1, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               6                 6
  CLUS_2               0                 5
  CLUS_3               1                 2

Clustering(7) Variable = 7q gain mutation analysis
D7V1, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               4                 8
  CLUS_2               1                 4
  CLUS_3               1                 2

Clustering(8) Variable = 8p gain mutation analysis
D8V1, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               4                 8
  CLUS_2               1                 4
  CLUS_3               2                 1

Clustering(9) Variable = 8q gain mutation analysis
D9V1, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               7                 5
  CLUS_2               2                 3
  CLUS_3               2                 1

Clustering(10) Variable = 9q gain mutation analysis
D10V1, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               3                 9
  CLUS_2               1                 4
  CLUS_3               0                 3

Clustering(11) Variable = 10p gain mutation analysis
D11V1, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                 11
  CLUS_2                1                  4
  CLUS_3                2                  1

Clustering(12) Variable = 12p gain mutation analysis
D12V1, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                8                  4
  CLUS_2                1                  4
  CLUS_3                0                  3

Clustering(13) Variable = 14q gain mutation analysis
D13V1, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                3                  9
  CLUS_2                0                  5
  CLUS_3                1                  2

Clustering(14) Variable = 17p gain mutation analysis
D14V1, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                5                  7
  CLUS_2                0                  5
  CLUS_3                0                  3

Clustering(15) Variable = 17q gain mutation analysis
D15V1, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                3                  9
  CLUS_2                0                  5
  CLUS_3                2                  1

Clustering(16) Variable = 18p gain mutation analysis
D16V1, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                3                  9
  CLUS_2                1                  4
  CLUS_3                0                  3

Clustering(17) Variable = 20p gain mutation analysis
D17V1, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                6                  6
  CLUS_2                3                  2
  CLUS_3                1                  2

Clustering(18) Variable = 20q gain mutation analysis
D18V1, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                6                  6
  CLUS_2                3                  2
  CLUS_3                1                  2

Clustering(19) Variable = 21q gain mutation analysis
D19V1, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                2                 10
  CLUS_2                1                  4
  CLUS_3                0                  3

Clustering(20) Variable = 22q gain mutation analysis
D20V1, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                3                  9
  CLUS_2                1                  4
  CLUS_3                1                  2

Clustering(21) Variable = Xq gain mutation analysis
D21V1, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               3                 9
  CLUS_2               1                 4
  CLUS_3               0                 3

Clustering(22) Variable = 3p loss mutation analysis
D22V1, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               5                 7
  CLUS_2               2                 3
  CLUS_3               0                 3

Clustering(23) Variable = 4p loss mutation analysis
D23V1, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               5                 7
  CLUS_2               1                 4
  CLUS_3               0                 3

Clustering(24) Variable = 4q loss mutation analysis
D24V1, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               5                 7
  CLUS_2               0                 5
  CLUS_3               0                 3

Clustering(25) Variable = 5p loss mutation analysis
D25V1, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               3                 9
  CLUS_2               0                 5
  CLUS_3               1                 2

Clustering(26) Variable = 5q loss mutation analysis
D26V1, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               3                 9
  CLUS_2               0                 5
  CLUS_3               1                 2

Clustering(27) Variable = 6p loss mutation analysis
D27V1, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               5                 7
  CLUS_2               1                 4
  CLUS_3               0                 3

Clustering(28) Variable = 6q loss mutation analysis
D28V1, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               2                10
  CLUS_2               1                 4
  CLUS_3               0                 3

Clustering(29) Variable = 9p loss mutation analysis
D29V1, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                11
  CLUS_2               1                 4
  CLUS_3               1                 2

Clustering(30) Variable = 10p loss mutation analysis
D30V1, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                3                  9
  CLUS_2                1                  4
  CLUS_3                0                  3

Clustering(31) Variable = 10q loss mutation analysis
D31V1, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                3                  9
  CLUS_2                0                  5
  CLUS_3                0                  3

Clustering(32) Variable = 11p loss mutation analysis
D32V1, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                3                  9
  CLUS_2                0                  5
  CLUS_3                0                  3

Clustering(33) Variable = 13q loss mutation analysis
D33V1, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                6                  6
  CLUS_2                1                  4
  CLUS_3                0                  3

Clustering(34) Variable = 16q loss mutation analysis
D34V1, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                3                  9
  CLUS_2                1                  4
  CLUS_3                0                  3

Clustering(35) Variable = 18p loss mutation analysis
D35V1, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                  9
  CLUS_2                1                  4
  CLUS_3                2                  1

Clustering(36) Variable = 18q loss mutation analysis
D36V1, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                4                  8
  CLUS_2                2                  3
  CLUS_3                1                  2

Clustering(37) Variable = 21q loss mutation analysis
D37V1, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                7                  5
  CLUS_2                1                  4
  CLUS_3                2                  1

Clustering(38) Variable = 22q loss mutation analysis
D38V1, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                2                 10
  CLUS_2                0                  5
  CLUS_3                1                  2
                V1 
"METHLYATION_CNMF" 
> q(save="no")
