
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/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.32.3479/Clusters2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.32.3479/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/LIHC/1590594/1.GDAC_mergedClustering.Finished/LIHC.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LIHC/1552289/1.GDAC_clinicalDataPicker.Finished/LIHC.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=1", "-MF=ALL", "-oT=", "-nV=Nozzle.R1", "-OP=AGGREGRATED_CLUSTER", "-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="
[1] "opt"                     "-OP=AGGREGRATED_CLUSTER"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  

nPatients in clinical file=62, in cluster file=54, common to both=45
[1]  2 45
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
 9 16 20 
 1  2  3 
 9 16 20 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
 8 29  8 
 1  2  3 
 8 29  8 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                     "DAYSTODEATH"                     
 [3] "DAYSTOLASTFOLLOWUP"               "VITALSTATUS"                     
 [5] "DCCUPLOADDATE"                    "PRIMARYSITEOFDESEASE"            
 [7] "GENDER"                           "DATEOFINITIALPATHOLOGICDIAGNOSIS"
 [9] "DAYSTOLASTKNOWNALIVE"             "HISTOLOGICALTYPE"                
[11] "NEOADJUVANTTHERAPY"               "BATCHNUMBER"                     

Input Data has 12 rows and 45 columns.

[1] "Batch" "12"   
[1] "Last Follow UP"
NULL
Variable 1:'AGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 2:'DAYSTODEATH':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'BATCH.NUMBER':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "VITALSTATUS" "GENDER"     
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 45 columns, 0 survival variables, and 2 non-survival variables.
VITALSTATUS, nv=2, binary=TRUE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MIRSEQ_CNMF
D1V1, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    5
  subtype2    8    8
  subtype3   12    8
   clus
vv  subtype1 subtype2 subtype3
  0        4        8       12
  1        5        8        8
D1V2, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    7
  subtype2    8    8
  subtype3    8   12
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        2        8        8
  MALE          7        8       12

Clustering(2) Variable = MIRSEQ_CHIERARCHICAL
D2V1, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    4
  subtype2   15   14
  subtype3    5    3
   clus
vv  subtype1 subtype2 subtype3
  0        4       15        5
  1        4       14        3
D2V2, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    6
  subtype2   14   15
  subtype3    2    6
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        2       14        2
  MALE          6       15        6
           V1            V2 
"VITALSTATUS"      "GENDER" 
> q(save="no")
