
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/Correlate_Cluster_cnvarms_onlysig/broadinstitute.org/cancer.genome.analysis/00508/6/CNV2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Cluster_cnvarms_onlysig/broadinstitute.org/cancer.genome.analysis/00508/6/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/cnvarms2cluster/DLBC-TP/3537843/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/DLBC-TP/3537831/DLBC-TP.transferedmergedcluster.txt", "-fF=", "-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=18, in cluster file=18, common to both=18
[1] "Reduce the number of clustering variables from 80 to 7."
[1]  7 18
[1] "3q gain"
[1] 3
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                3                15 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                3                15 
[1] "7p gain"
[1] 3
      7P GAIN CNV 7P GAIN WILD-TYPE 
                4                14 
      7P GAIN CNV 7P GAIN WILD-TYPE 
                4                14 
[1] "7q gain"
[1] 3
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
                3                15 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
                3                15 
[1] "11q gain"
[1] 3
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 4                 14 
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 4                 14 
[1] "18p gain"
[1] 3
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 3                 15 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 3                 15 
[1] "18q gain"
[1] 3
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 3                 15 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 3                 15 
[1] "21q gain"
[1] 3
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 5                 13 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 5                 13 
[1] "data2feature, selection="
[1] "METHLYATION_CNMF"

Input Data has 1 rows and 18 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 18 columns, 0 survival variables, and 1 non-survival variables.
METHLYATION_CNMF, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 3q gain
D1V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN CNV          1    2
  3Q GAIN WILD-TYPE    8    7
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           1                 8
  CLUS_2           2                 7

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

Clustering(3) Variable = 7q gain
D3V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN CNV          1    2
  7Q GAIN WILD-TYPE    8    7
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           1                 8
  CLUS_2           2                 7

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

Clustering(5) Variable = 18p gain
D5V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN CNV          1    2
  18P GAIN WILD-TYPE    8    7
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            1                  8
  CLUS_2            2                  7

Clustering(6) Variable = 18q gain
D6V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN CNV          1    2
  18Q GAIN WILD-TYPE    8    7
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            1                  8
  CLUS_2            2                  7

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