
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_mergedClustering/PCPG-TP/8282704/PCPG-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PCPG-TP/8143061/PCPG-TP.merged_data.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=.05", "-cQ=0.25", "-MF=ALL", "-oT=PCPG-TP", "-nV=Nozzle.R1", "-OP=AGGREGRATED_CLUSTER", "-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=PCPG-TP"
[1] "opt"                     "-OP=AGGREGRATED_CLUSTER"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PCPG-TP/8143061/PCPG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PCPG-TP/8282704/PCPG-TP.mergedcluster.txt"

nPatients in clinical file=10, in cluster file=179, common to both=10
[1] "Reduce the number of clustering variables from 6 to 4."
[1]  4 10
[1] "CN_CNMF"
[1] 3
3 4 
4 5 
3 4 
4 5 
[1] "MIRSEQ_CNMF"
[1] 3
1 2 3 
3 5 2 
1 2 
3 5 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
1 2 3 4 
1 3 4 2 
2 3 
3 4 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
1 2 3 
4 3 3 
1 2 3 
4 3 3 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
[1] "YEARSTOBIRTH"       "VITALSTATUS"        "DAYSTODEATH"       
[4] "DAYSTOLASTFOLLOWUP" "DCCUPLOADDATE"      "GENDER"            
[7] "RADIATIONTHERAPY"   "BATCHNUMBER"       

Input Data has 8 rows and 10 columns.

[1] "Batch" "8"    
[1] "Last Follow UP"
TCGA-PR-A5PF TCGA-PR-A5PG TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
         240         1094          773          211           55           22 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q 
         766           70          134           24 
Variable 1:'AGE':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTODEATH':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'BATCH.NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"    "GENDER"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 10 columns, 0 survival variables, and 2 non-survival variables.
AGE, nv=9, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, continuous
D1V2, binary
          cls
clus       0 1
  subtype3 3 1
  subtype4 3 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype3    3    1
  subtype4    3    2
        clus
vv       subtype3 subtype4
  FEMALE        3        3
  MALE          1        2

Clustering(2) Variable = MIRSEQ_CNMF
D2V1, continuous
D2V2, binary
          cls
clus       0 1
  subtype1 2 1
  subtype2 4 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    1
  subtype2    4    1
        clus
vv       subtype1 subtype2
  FEMALE        2        4
  MALE          1        1

Clustering(3) Variable = MIRSEQ_CHIERARCHICAL
D3V1, continuous
D3V2, binary
          cls
clus       0 1
  subtype2 3 0
  subtype3 2 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype2    3    0
  subtype3    2    2
        clus
vv       subtype2 subtype3
  FEMALE        3        2
  MALE          0        2

Clustering(4) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D4V1, continuous
D4V2, binary
          cls
clus       0 1
  subtype1 2 2
  subtype2 3 0
  subtype3 2 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    2
  subtype2    3    0
  subtype3    2    1
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        2        3        2
  MALE          2        0        1
> q(save="no")
