
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/UCEC-TP/4403448/UCEC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/UCEC-TP/4435033/UCEC-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=957, in expression file=118, common to both=85
Number of genes in original expression dataset=18332
[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] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "BATCHNUMBER"                           

Input Data has 18 rows and 85 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
        1104         2768           NA          161          156          223 
TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
         455           33           31           15           34           31 
TCGA-AJ-A3BH TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
          NA           61           51           NA           64           65 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
          50           39           28          210           78           41 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
          52           23           59          142           57           56 
TCGA-AJ-A3TW TCGA-AP-A3K1 TCGA-AX-A2H4 TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT 
          51          555           NA           NA            7            3 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
          10            4            6           NA            1            4 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
          NA            7           36          254          440            4 
TCGA-B5-A1MS TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-BG-A0MK TCGA-BG-A3EW TCGA-BG-A3PP 
          NA         1890          152           NA          344          207 
TCGA-BK-A13B TCGA-BK-A4ZD TCGA-BK-A56F TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
         966          211          200            8          130          125 
TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EO-A22U TCGA-EO-A22X 
          NA         2797           NA          202          825          981 
TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EY-A2ON TCGA-EY-A2OO 
         761         1046          589          392          409         1392 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 
         943          884          258          421          196          544 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-FI-A3PV TCGA-K6-A3WQ TCGA-KJ-A3U4 
          65          212          113           NA          203           73 
TCGA-PG-A5BC 
         329 
Variable 1:'AGE':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=68,	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=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "HISTOLOGICAL.TYPE"                     
[3] "RADIATIONS.RADIATION.REGIMENINDICATION"
[4] "COMPLETENESS.OF.RESECTION"             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 85 columns, 1 survival variables, and 4 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
STXBP6|29091 
       15459 
AGE, nv=39, binary=FALSE, numeric=TRUE
CAMK2B|816 
      2711 
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
HIF3A|64344 
       7216 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
P2RY4|5030 
     11464 
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
IGFBP1|3484 
       7689 
> q(save="no")
