
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/KIRP-TP/6068695/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRP-TP/6159654/KIRP-TP.transferedmergedcluster.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ALL", "-oT=KIRP-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=KIRP-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/KIRP-TP/6159654/KIRP-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRP-TP/6068695/transformed.cor.cli.txt"

nPatients in clinical file=172, in cluster file=112, common to both=112
[1] "Reduce the number of clustering variables from 2 to 1."
[1]   1 112
[1] "NF2 MUTATION ANALYSIS"
[1] 3
  NF2 MUTATED NF2 WILD-TYPE 
            7           105 
  NF2 MUTATED NF2 WILD-TYPE 
            7           105 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
[1] "CN_CNMF"                     "METHLYATION_CNMF"           
[3] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
[5] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[7] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 8 rows and 112 columns.

Variable 1:'CN_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"                     "METHLYATION_CNMF"           
[3] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
[5] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[7] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 112 columns, 0 survival variables, and 8 non-survival variables.
CN_CNMF, nv=4, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = NF2 MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NF2 MUTATED        0      3      0      4
  NF2 WILD-TYPE     20     48     20     17
D1V1, multiclass
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  CLUS_1           0            20
  CLUS_2           3            48
  CLUS_3           0            20
  CLUS_4           4            17
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF2 MUTATED        0      5      2
  NF2 WILD-TYPE     28     26     36
D1V2, multiclass
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  CLUS_1           0            28
  CLUS_2           5            26
  CLUS_3           2            36
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NF2 MUTATED        5      2      0      0
  NF2 WILD-TYPE     36     23     17     20
D1V3, multiclass
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  CLUS_1           5            36
  CLUS_2           2            23
  CLUS_3           0            17
  CLUS_4           0            20
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF2 MUTATED        3      2      2
  NF2 WILD-TYPE     20     42     34
D1V4, multiclass
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  CLUS_1           3            20
  CLUS_2           2            42
  CLUS_3           2            34
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF2 MUTATED        2      3      2
  NF2 WILD-TYPE     39     42     24
D1V5, multiclass
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  CLUS_1           2            39
  CLUS_2           3            42
  CLUS_3           2            24
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF2 MUTATED        2      2      3
  NF2 WILD-TYPE     14     47     44
D1V6, multiclass
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  CLUS_1           2            14
  CLUS_2           2            47
  CLUS_3           3            44
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF2 MUTATED        3      3      1
  NF2 WILD-TYPE     39     47     19
D1V7, multiclass
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  CLUS_1           3            39
  CLUS_2           3            47
  CLUS_3           1            19
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF2 MUTATED        0      4      3
  NF2 WILD-TYPE     12     49     44
D1V8, multiclass
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  CLUS_1           0            12
  CLUS_2           4            49
  CLUS_3           3            44
> q(save="no")
