
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.14.3949/ClinicalAnalysisAllGenes.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ClinicalAnalysisAllGenes_new.14.3949/", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/PAAD-TP/4426526/PAAD-TP.meth.by_min_expr_corr.data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/PAAD-TP/4434820/PAAD-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=50, in expression file=65, common to both=50
Number of genes in original expression dataset=20445
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "RADIATIONTHERAPY"                      
[14] "HISTOLOGICALTYPE"                      
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "NUMBERPACKYEARSSMOKED"                 
[17] "YEAROFTOBACCOSMOKINGONSET"             
[18] "COMPLETENESS.OF.RESECTION"             
[19] "NUMBER.OF.LYMPH.NODES"                 
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 50 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A4P6 TCGA-FB-A545 
          NA          153          158            4            7            1 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 
         392          232          239           28           20           NA 
TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
           4            8          369          366            8           19 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          30           21           NA           28           15            3 
TCGA-HZ-8636 TCGA-HZ-8637 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
           5           NA           90           23           31           NA 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
         182           46          347           NA           NA           NA 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
          NA           NA          476          851           NA           NA 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
          NA           NA           NA          488           NA           NA 
TCGA-IB-8126 TCGA-IB-8127 
          17          521 
Variable 1:'AGE':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'NUMBERPACKYEARSSMOKED':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'COMPLETENESS.OF.RESECTION':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                       "NEOPLASM.DISEASESTAGE"    
 [3] "PATHOLOGY.T.STAGE"         "PATHOLOGY.N.STAGE"        
 [5] "PATHOLOGY.M.STAGE"         "GENDER"                   
 [7] "HISTOLOGICAL.TYPE"         "NUMBERPACKYEARSSMOKED"    
 [9] "YEAROFTOBACCOSMOKINGONSET" "COMPLETENESS.OF.RESECTION"
[11] "NUMBER.OF.LYMPH.NODES"    
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 50 columns, 1 survival variables, and 11 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
HIST1H2AD__1 
        7852 
AGE, nv=31, binary=FALSE, numeric=TRUE
MAP3K12 
  10506 
NEOPLASM.DISEASESTAGE, nv=6, binary=FALSE, numeric=FALSE
GRM4 
7487 
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
SLC25A13 
   16299 
[1] "PATHOLOGY.T.STAGE"
[1] "num to class table"
vv1
 1  2  3  4 
 2  3 43  2 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
KPNA7 
 9255 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GRM4 
7487 
GENDER, nv=2, binary=FALSE, numeric=FALSE
CCNYL1 
  3375 
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
SPAG8 
16967 
NUMBERPACKYEARSSMOKED, nv=10, binary=FALSE, numeric=TRUE
BAG4 
1362 
YEAROFTOBACCOSMOKINGONSET, nv=11, binary=FALSE, numeric=TRUE
 RFX3 
14950 
COMPLETENESS.OF.RESECTION, nv=3, binary=FALSE, numeric=FALSE
ZNF551 
 20155 
NUMBER.OF.LYMPH.NODES, nv=12, binary=FALSE, numeric=TRUE
WDR88 
19470 
> q(save="no")
