
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/THCA/1729562/0.GDAC_RPPA_preprocess.Finished/THCA.rppa.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/THCA/1709390/1.GDAC_clinicalDataPicker.Finished/THCA.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=197, in expression file=224, common to both=152
Number of genes in original expression dataset=175
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "HISTOLOGICALTYPE"                      
[10] "RADIATIONS.RADIATION.REGIMENINDICATION"
[11] "NEOADJUVANTTHERAPY"                    
[12] "BATCHNUMBER"                           

Input Data has 12 rows and 152 columns.

[1] "Batch" "12"   
[1] "Last Follow UP"
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
         479          356          232          182          197          251 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZF TCGA-BJ-A0ZG 
         264          122          183          237          210          230 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
         152           85           13          235          246          148 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME 
          84          155           16            3            6            7 
TCGA-DE-A0Y2 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13R 
         231          161          286          274          215           92 
TCGA-DJ-A13S TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
         265          362          454          243          334         3041 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
         549          212          151          212           30          273 
TCGA-DJ-A1QO TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PR TCGA-DJ-A2PS 
          31          304          242          152          318           59 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
         312          242          234          267          256          247 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
         284          287          301          291          215          315 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY 
         378          330          304         1225           93          945 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A2EA 
         365         1544         1222          635          427           11 
TCGA-E8-A2JQ TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
          NA          153          214           NA          245          217 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J 
         284         1421         1209          650           81          207 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
         138          106          189          192          348          249 
TCGA-EM-A2CL TCGA-EM-A2CM TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
         209          357          344          183           90          199 
TCGA-EM-A2CR TCGA-EM-A2CS TCGA-EM-A2CU TCGA-ET-A25G TCGA-ET-A25L TCGA-ET-A25M 
         218          284          176         1088          450          375 
TCGA-ET-A25O TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 
         135          579          373         1049          449           43 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
        1182            9          362           59         2266         2535 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BS 
         406         1413          237           51          127          168 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
         752           39           56           72          137         2095 
TCGA-ET-A3DP TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DV TCGA-ET-A3DW TCGA-FE-A22Z 
        1536            9          145         3424          751         1565 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
        1442          374         1346          751         1333         3130 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A239 TCGA-FE-A23A TCGA-FY-A2QD TCGA-FY-A3BL 
        2031         2292           NA         1907           38           35 
TCGA-FY-A3ON TCGA-GE-A2C6 TCGA-H2-A2K9 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-J8-A3NZ 
          46          206          145         1070          939           68 
TCGA-J8-A3O0 TCGA-J8-A3O1 
         392          415 
Variable 1:'AGE':	nDistinctValues=62,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=136,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=TRUE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=3,	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=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'BATCH.NUMBER':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "HISTOLOGICAL.TYPE"                     
[4] "RADIATIONS.RADIATION.REGIMENINDICATION"
[5] "NEOADJUVANT.THERAPY"                   
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 152 columns, 1 survival variables, and 5 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
[1] "Survival variable Time to Death has too few event occurrence, nEvent=1"
AGE, nv=62, binary=FALSE, numeric=TRUE
SNAI2|SNAIL-M-C 
            131 
GENDER, nv=2, binary=FALSE, numeric=FALSE
AR|AR-R-V 
       12 
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
ANXA1|ANNEXIN_I-R-V 
                 19 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
ERBB2|HER2_PY1248-R-V 
                   70 
NEOADJUVANT.THERAPY, nv=2, binary=FALSE, numeric=FALSE
NF2|NF2-R-C 
         94 
> q(save="no")
