
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/GDAC_RPPA_preprocess/GBM-TP/2540066/0.GDAC_RPPA_preprocess.Finished/GBM-TP.rppa.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/GBM-TP/2540063/1.GDAC_clinicalDataPicker.Finished/GBM-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=565, in expression file=214, common to both=210
Number of genes in original expression dataset=171
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "KARNOFSKYPERFORMANCESCORE"             
[10] "HISTOLOGICALTYPE"                      
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "BATCHNUMBER"                           

Input Data has 12 rows and 210 columns.

[1] "Batch" "12"   
[1] "Last Follow UP"
TCGA-02-0003 TCGA-02-0004 TCGA-02-0011 TCGA-02-0014 TCGA-02-0068 TCGA-02-0069 
         144          345          630         2511          804          873 
TCGA-02-0116 TCGA-02-2470 TCGA-02-2485 TCGA-06-0125 TCGA-06-0126 TCGA-06-0128 
        1489          393          469         1439            3          691 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0154 TCGA-06-0155 TCGA-06-0156 TCGA-06-0171 
         988          320          389          263          164          396 
TCGA-06-0189 TCGA-06-0238 TCGA-06-0644 TCGA-06-0650 TCGA-06-0875 TCGA-06-0876 
         454          359          375          717          279          271 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
         204          218          699          165          637          226 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
         193          109          815          239          413          127 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
          33           23          149           86          259          181 
TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 
         207          182          133          285          341          107 
TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 
         254          138          268          273          260          204 
TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
         155           83          114          186          138          119 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 TCGA-06-6694 TCGA-06-6695 
         236          163           44           15          224          252 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-08-0245 
         391          145           47          145          151         1057 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 
        3310           53          132          419          316          231 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
         103         1636           39          195          458          685 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0360 TCGA-08-0373 
         447         1084          593           29          352          134 
TCGA-08-0375 TCGA-08-0380 TCGA-08-0385 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 
         279          330           31          478           97          322 
TCGA-08-0392 TCGA-12-0691 TCGA-12-0692 TCGA-12-1597 TCGA-12-1598 TCGA-12-1599 
           9          185           80          427          287          769 
TCGA-12-3646 TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 
        1314          351          333          358         1050          357 
TCGA-12-5295 TCGA-12-5301 TCGA-14-0813 TCGA-14-0862 TCGA-14-0871 TCGA-14-1823 
         398           61           41           88          879          542 
TCGA-15-1446 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-1460 TCGA-19-0957 
         581         1618          167          119          195          665 
TCGA-19-0962 TCGA-19-1386 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 
          13          276          141          772          106          217 
TCGA-19-1788 TCGA-19-1789 TCGA-19-1790 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
         111           99          153            4          294          148 
TCGA-19-2625 TCGA-19-2631 TCGA-19-4068 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
         124          213          136          202          343          244 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 
         567          144          242           54          198          164 
TCGA-19-5959 TCGA-19-5960 TCGA-26-1440 TCGA-26-1442 TCGA-26-5132 TCGA-26-5133 
         161          165          296          953          286          452 
TCGA-26-5134 TCGA-26-6173 TCGA-26-6174 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
         167          241           70          146          504           NA 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1836 TCGA-27-2518 TCGA-27-2528 TCGA-28-1746 
         555         1008          914          752          479            6 
TCGA-28-1747 TCGA-28-1750 TCGA-28-1752 TCGA-28-1753 TCGA-28-1757 TCGA-28-1760 
          77          253          257           36            4          143 
TCGA-28-5208 TCGA-28-5214 TCGA-32-1970 TCGA-32-1976 TCGA-32-1978 TCGA-32-1982 
         473          432          467           15          482          142 
TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 TCGA-32-4210 TCGA-32-4211 TCGA-32-5222 
         386          451          515          112          383          165 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 
         272          290           30          135          183            6 
TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
         351          235          105          533          131          436 
TCGA-74-6581 TCGA-74-6584 TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 
         250          227          138          535           94          111 
TCGA-76-4931 TCGA-76-4932 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 
         278         1458          100           82          519          253 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
         147          153          281          234          236           49 
Variable 1:'AGE':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=126,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=190,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=4,	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=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'BATCH.NUMBER':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "KARNOFSKY.PERFORMANCE.SCORE"           
[4] "RADIATIONS.RADIATION.REGIMENINDICATION"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 210 columns, 1 survival variables, and 4 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
PTGS2|COX-2-R-C 
             34 
AGE, nv=57, binary=FALSE, numeric=TRUE
ANXA1|ANNEXIN_I-R-V 
                 18 
GENDER, nv=2, binary=FALSE, numeric=FALSE
SHC1|SHC_PY317-R-NA 
                124 
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
CDH1|E-CADHERIN-R-V 
                 52 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
IGFBP2|IGFBP2-R-V 
               76 
> q(save="no")
