
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/ClinicalAnalysisAllGenes_new.13.3873/ClinicalAnalysisAllGenes.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ClinicalAnalysisAllGenes_new.13.3873/", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/READ-TP/2398254/0.mRNAseq_preprocessor.Finished/READ-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/READ-TP/2332161/1.GDAC_clinicalDataPicker.Finished/READ-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=168, in expression file=72, common to both=72
Number of genes in original expression dataset=17926
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "HISTOLOGICALTYPE"                      
[11] "PATHOLOGICSPREAD(PT)"                  
[12] "PATHOLOGICSPREAD(PN)"                  
[13] "PATHOLOGICSPREAD(M)"                   
[14] "TUMORSTAGE"                            
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 72 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 
         323          412          387          316           NA           NA 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
          NA           NA           31           31           61           NA 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
          NA           31           NA           NA           NA           30 
TCGA-AG-3600 TCGA-AG-3601 TCGA-AG-3602 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
          NA           NA           NA           NA           NA           NA 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3878 
          NA           NA           31           29           NA           30 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
          NA           NA           NA           NA           28           NA 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
          31           30           30           NA           NA           NA 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
          NA           31           31           NA           31           31 
TCGA-AG-4015 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
          NA          637          423          183          789          700 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
         518          484          396           31           31          365 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
         365         2130         1946          334         1581         1519 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
          59         1184         1884         1246         1156         2192 
Variable 1:'AGE':	nDistinctValues=35,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=30,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=5,	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=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'PATHOLOGY.T':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'PATHOLOGY.N':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'PATHOLOGICSPREAD(M)':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                 "GENDER"              "HISTOLOGICAL.TYPE"  
[4] "PATHOLOGY.T"         "PATHOLOGY.N"         "PATHOLOGICSPREAD(M)"
[7] "TUMOR.STAGE"        
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
 1  2  3  4 
18 25 18 10 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 72 columns, 1 survival variables, and 7 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
GHRLOS|100126793 
            6286 
AGE, nv=35, binary=FALSE, numeric=TRUE
PI3|5266 
   11617 
GENDER, nv=2, binary=FALSE, numeric=FALSE
XIST|7503 
    17097 
HISTOLOGICAL.TYPE, nv=2, binary=FALSE, numeric=FALSE
EFNA5|1946 
      4854 
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
UTP23|84294 
      16771 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
T1 T2 T3 T4 
 5 15 48  4 
PATHOLOGY.N, nv=3, binary=FALSE, numeric=TRUE
HES5|388585 
       6957 
[1] "PATHOLOGY.N"
[1] "num to class table"
vv1
N0 N1 N2 
44 16 12 
PATHOLOGICSPREAD(M), nv=2, binary=FALSE, numeric=FALSE
SCN2A|6326 
     13635 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
HES5|388585 
       6957 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
     18      25      18      10 
> q(save="no")
