
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/LGG-TP/2282463/0.mRNAseq_preprocessor.Finished/LGG-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LGG-TP/2172584/1.GDAC_clinicalDataPicker.Finished/LGG-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=208, in expression file=110, common to both=110
Number of genes in original expression dataset=18308
[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] "KARNOFSKYPERFORMANCESCORE"             
[11] "HISTOLOGICALTYPE"                      
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "BATCHNUMBER"                           

Input Data has 13 rows and 110 columns.

[1] "Batch" "13"   
[1] "Last Follow UP"
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5396 
         234         1335          481          323         1965          289 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 
         546          257          229          243          224          200 
TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5279 TCGA-DB-5280 
        2977         1786         1726         1458         1354          404 
TCGA-DB-5281 TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5143 TCGA-DU-5847 TCGA-DU-5849 
        1614          607          968          438          547          442 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 
         530           NA          257          207         5546          576 
TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6395 
         531          460         6423         1219          682         1491 
TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 
        2286         1401           NA           37         2660          213 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
         354           NA          605          511         2875         3469 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
         242          234           NA           NA         4752         4205 
TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7013 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
          NA           NA           NA           NA          800           NA 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 
          NA         2868           NA           NA           NA           NA 
TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
        1525         2051         1251         2432         1762         4084 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 
        2378         2907         3978          160          787          407 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
         377          979          220          189          142          102 
TCGA-FG-6692 TCGA-FG-7637 TCGA-FG-7638 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7472 
         126          802          233            3          146            1 
TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 
         503          114          446          199          194           13 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7603 TCGA-HT-7604 
        1800         1644         4687          121          705         3283 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7491 TCGA-HW-7493 
        1399         1706          608          409          854          285 
TCGA-HW-7495 TCGA-IK-7675 
          13           NA 
Variable 1:'AGE':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=41,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=91,	numeric=TRUE,	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=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=91,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'BATCH.NUMBER':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "KARNOFSKY.PERFORMANCE.SCORE"           
[4] "HISTOLOGICAL.TYPE"                     
[5] "RADIATIONS.RADIATION.REGIMENINDICATION"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 110 columns, 1 survival variables, and 5 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
PGAM1|5223 
     11876 
AGE, nv=45, binary=FALSE, numeric=TRUE
TRMT2B|79979 
       16607 
GENDER, nv=2, binary=FALSE, numeric=FALSE
XIST|7503 
    17460 
KARNOFSKY.PERFORMANCE.SCORE, nv=5, binary=FALSE, numeric=TRUE
C8ORF76|84933 
         2534 
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "num to class table"
vv1
 50  70  80  90 100 
  2   3  10  27  16 
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
AK2|204 
    446 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
C9ORF93|203238 
          2611 
> q(save="no")
