
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-TP/2590905/0.GDAC_RPPA_preprocess.Finished/THCA-TP.rppa.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/THCA-TP/2589062/1.GDAC_clinicalDataPicker.Finished/THCA-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=290, in expression file=224, common to both=163
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] "RADIATIONTHERAPY"                      
[10] "HISTOLOGICALTYPE"                      
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "RADIATIONEXPOSURE"                     
[13] "DISTANT.METASTASIS"                    
[14] "EXTRATHYROIDAL.EXTENSION"              
[15] "LYMPH.NODE.METASTASIS"                 
[16] "COMPLETENESS.OF.RESECTION"             
[17] "NUMBER.OF.LYMPH.NODES"                 
[18] "TUMOR.STAGECODE"                       
[19] "NEOPLASM.DISEASESTAGE"                 
[20] "MULTIFOCALITY"                         
[21] "TUMOR.SIZE"                            
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 163 columns.

[1] "Batch" "22"   
[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-BJ-A290 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
          84          155          626           16            3            6 
TCGA-CE-A3ME TCGA-DE-A0Y2 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DJ-A13M TCGA-DJ-A13O 
           7          231          161          286          274          215 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
          92          265          362          454          243          334 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
        3041          549          212          151          212           30 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
         273           31          304          242          152          623 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PY 
         318           59          312          242          234          267 
TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
         256          247          284          206          287          301 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
         262          291          215          315          378          330 
TCGA-DJ-A2QC TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
         304         1225           93          945          365         1544 
TCGA-E3-A3E1 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-EM-A1CT 
        1222          635          427           11           NA          153 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
         214           NA          245          217          284         1421 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22L TCGA-EM-A22M 
        1209          650           81          207          138          106 
TCGA-EM-A22O TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CM 
         189          192          348          249          209          357 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CS 
         344          183           90          199          218          284 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OY TCGA-EM-A2P1 TCGA-EM-A3AJ TCGA-EM-A3AN 
         176          353          347          194          397          341 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-ET-A25G TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25O 
         336          161         1088          450          375          135 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A2N5 
         579          373         1049          449           43         1182 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39P 
           9          362           59         2266         2535          406 
TCGA-ET-A39R TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BS TCGA-ET-A3BT 
        1413          237           51          127          168          752 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
          39           56           72          137         2095         1536 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DV TCGA-ET-A3DW TCGA-FE-A22Z TCGA-FE-A230 
           9          145         3424          751         1565         1442 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
         374         1346          751         1333         3130         2031 
TCGA-FE-A237 TCGA-FE-A239 TCGA-FE-A23A TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3ON 
        2292           NA         1907           38           35           46 
TCGA-GE-A2C6 TCGA-H2-A2K9 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-J8-A3NZ TCGA-J8-A3O0 
         206          145         1070          939           68          392 
TCGA-J8-A3O1 
         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=145,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=TRUE.
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=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RADIATIONEXPOSURE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'DISTANT.METASTASIS':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'EXTRATHYROIDAL.EXTENSION':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'LYMPH.NODE.METASTASIS':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'COMPLETENESS.OF.RESECTION':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'TUMOR.STAGECODE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NEOPLASM.DISEASESTAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'MULTIFOCALITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'TUMOR.SIZE':	nDistinctValues=53,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "GENDER"                                
 [3] "HISTOLOGICAL.TYPE"                     
 [4] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [5] "RADIATIONEXPOSURE"                     
 [6] "DISTANT.METASTASIS"                    
 [7] "EXTRATHYROIDAL.EXTENSION"              
 [8] "LYMPH.NODE.METASTASIS"                 
 [9] "COMPLETENESS.OF.RESECTION"             
[10] "NUMBER.OF.LYMPH.NODES"                 
[11] "TUMOR.STAGECODE"                       
[12] "NEOPLASM.DISEASESTAGE"                 
[13] "MULTIFOCALITY"                         
[14] "TUMOR.SIZE"                            
[1] "TUMOR.?STAGE" "11"          
[1] "stage2"
vv
 T1 T1A T1B  T2  T3 T4A 
 14   3  22  69  52   3 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 163 columns, 1 survival variables, and 14 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 
RADIATIONEXPOSURE, nv=2, binary=FALSE, numeric=FALSE
AKT1S1|PRAS40_PT246-R-V 
                    109 
DISTANT.METASTASIS, nv=3, binary=FALSE, numeric=FALSE
BCL2L1|BCL-XL-R-V 
               25 
EXTRATHYROIDAL.EXTENSION, nv=3, binary=FALSE, numeric=FALSE
BECN1|BECLIN-G-V 
              26 
LYMPH.NODE.METASTASIS, nv=5, binary=FALSE, numeric=FALSE
ANXA1|ANNEXIN_I-R-V 
                 19 
COMPLETENESS.OF.RESECTION, nv=3, binary=FALSE, numeric=FALSE
EIF4EBP1|4E-BP1_PS65-R-V 
                       3 
NUMBER.OF.LYMPH.NODES, nv=21, binary=FALSE, numeric=TRUE
DVL3|DVL3-R-V 
           52 
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
[1] "Clinical variable TUMOR.STAGECODE has too few non-missing values, n=0"
NEOPLASM.DISEASESTAGE, nv=5, binary=FALSE, numeric=FALSE
MAP2K1|MEK1-R-V 
             85 
MULTIFOCALITY, nv=2, binary=FALSE, numeric=FALSE
YAP1|YAP-R-V 
         149 
TUMOR.SIZE, nv=53, binary=FALSE, numeric=TRUE
NOTCH3|NOTCH3-R-C 
               96 
> q(save="no")
