
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/BLCA-TP/6068629/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BLCA-TP/6159655/BLCA-TP.transferedmergedcluster.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ALL", "-oT=BLCA-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=BLCA-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/BLCA-TP/6159655/BLCA-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/6068629/transformed.cor.cli.txt"

nPatients in clinical file=242, in cluster file=28, common to both=28
[1]  1 28
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            11             17 
  TP53 MUTATED TP53 WILD-TYPE 
            11             17 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 10 rows and 28 columns.

Variable 1:'CN_CNMF':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'RPPA_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'RPPA_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_MATURE_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 28 columns, 0 survival variables, and 10 non-survival variables.
CN_CNMF, nv=6, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=5, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=4, 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=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  TP53 MUTATED        1      3      1      2      2      1
  TP53 WILD-TYPE      2      8      2      2      2      0
D1V1, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        3      5      3
  TP53 WILD-TYPE      3      7      7
D1V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3              3
  CLUS_2            5              7
  CLUS_3            3              7
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TP53 MUTATED        1      1      8      0      1
  TP53 WILD-TYPE      5      4      3      1      1
D1V3, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        3      0      5      3
  TP53 WILD-TYPE      7      1      2      4
D1V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3              7
  CLUS_2            0              1
  CLUS_3            5              2
  CLUS_4            3              4
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        2      6      3      0
  TP53 WILD-TYPE      3      5      1      8
D1V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2              3
  CLUS_2            6              5
  CLUS_3            3              1
  CLUS_4            0              8
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        3      2      6
  TP53 WILD-TYPE      7      3      7
D1V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3              7
  CLUS_2            2              3
  CLUS_3            6              7
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        2      3      6
  TP53 WILD-TYPE      5      5      7
D1V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2              5
  CLUS_2            3              5
  CLUS_3            6              7
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        8      2      1
  TP53 WILD-TYPE     12      0      5
D1V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            8             12
  CLUS_2            2              0
  CLUS_3            1              5
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        2      5      2      2
  TP53 WILD-TYPE      5      4      3      5
D1V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2              5
  CLUS_2            5              4
  CLUS_3            2              3
  CLUS_4            2              5
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        5      2      3      1
  TP53 WILD-TYPE      6      4      2      5
D1V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            5              6
  CLUS_2            2              4
  CLUS_3            3              2
  CLUS_4            1              5
> q(save="no")
