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

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/334895/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/DLBC-TP/2666534/1.GDAC_mergedClustering.Finished/DLBC-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=DLBC-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=DLBC-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=17, in cluster file=18, common to both=17
[1] "Reduce the number of clustering variables from 80 to 7."
[1]  7 17
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                14 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                14 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                4                13 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                4                13 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                3                14 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                3                14 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                 13 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                 13 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 14 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 14 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 14 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 14 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                 12 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                 12 
[1] "data2feature, selection=ALL"
[1] "METHLYATION_CNMF"

Input Data has 1 rows and 17 columns.

Variable 1:'METHLYATION_CNMF':	nDistinctValues=2,	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 17 columns, 0 survival variables, and 1 non-survival variables.
METHLYATION_CNMF, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 3q gain mutation analysis
D1V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      2    1
  3Q GAIN WILD-TYPE    7    7
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               1                 7

Clustering(2) Variable = 7p gain mutation analysis
D2V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      2    2
  7P GAIN WILD-TYPE    7    6
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               2                 6

Clustering(3) Variable = 7q gain mutation analysis
D3V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2    1
  7Q GAIN WILD-TYPE    7    7
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               1                 7

Clustering(4) Variable = 11q gain mutation analysis
D4V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      2    2
  11Q GAIN WILD-TYPE    7    6
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                2                  7
  CLUS_2                2                  6

Clustering(5) Variable = 18p gain mutation analysis
D5V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2    1
  18P GAIN WILD-TYPE    7    7
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                2                  7
  CLUS_2                1                  7

Clustering(6) Variable = 18q gain mutation analysis
D6V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2    1
  18Q GAIN WILD-TYPE    7    7
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                  7
  CLUS_2                1                  7

Clustering(7) Variable = 21q gain mutation analysis
D7V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    2
  21Q GAIN WILD-TYPE    6    6
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                3                  6
  CLUS_2                2                  6
                V1 
"METHLYATION_CNMF" 
> q(save="no")
