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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_mRNA_Preprocess_Median/UCEC-TP/2666698/0.GDAC_mRNA_Preprocess_Median.Finished/UCEC-TP.medianexp.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/UCEC-TP/2589075/1.GDAC_clinicalDataPicker.Finished/UCEC-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=455, in expression file=54, common to both=54
Number of genes in original expression dataset=17814
[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] "TUMORGRADE"                            
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "COMPLETENESS.OF.RESECTION"             
[14] "BATCHNUMBER"                           

Input Data has 14 rows and 54 columns.

[1] "Batch" "14"   
[1] "Last Follow UP"
TCGA-A5-A0G2 TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GE 
        4053         1079          790           NA          275         2717 
TCGA-A5-A0GH TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GU TCGA-AP-A051 TCGA-AP-A052 
        1671         1448         1087          495         2545           NA 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
         181           NA         2026         1198         1364          831 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
         639          239          260           NA         3443         2906 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LN TCGA-AP-A0LT TCGA-AP-A0LV 
        1921           NA          965         1992         1185          385 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
          NA          603          902         2078         2191         1413 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06F 
        1075         1398         2024         1064         1639         1554 
TCGA-AX-A06J TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-B5-A0JR TCGA-B5-A0JZ TCGA-B5-A0K0 
         913         1148         2004         1465          689          679 
TCGA-B5-A0K1 TCGA-B5-A0K4 TCGA-BG-A0LW TCGA-BG-A0MI TCGA-BK-A0C9 TCGA-BK-A0CC 
         746          466          194           NA          289          211 
Variable 1:'AGE':	nDistinctValues=32,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=47,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'TUMOR.GRADE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'BATCH.NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "HISTOLOGICAL.TYPE"                     
[3] "TUMOR.GRADE"                           
[4] "RADIATIONS.RADIATION.REGIMENINDICATION"
[5] "COMPLETENESS.OF.RESECTION"             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE" "3"           
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 54 columns, 1 survival variables, and 4 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
KRT1 
6788 
AGE, nv=32, binary=FALSE, numeric=TRUE
TMEM79 
  7050 
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
KLHL34 
 12015 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
GCDH 
2801 
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RHOXF1 
 12283 
> q(save="no")
