
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.14.3949/ClinicalAnalysisAllGenes.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ClinicalAnalysisAllGenes_new.14.3949/", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/PRAD-TP/3527760/PRAD-TP.meth.by_min_expr_corr.data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/PRAD-TP/3352982/PRAD-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=154, in expression file=198, common to both=153
Number of genes in original expression dataset=20063
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                     "DAYSTODEATH"                     
 [3] "DAYSTOLASTFOLLOWUP"               "VITALSTATUS"                     
 [5] "DCCUPLOADDATE"                    "PRIMARYSITEOFDESEASE"            
 [7] "GENDER"                           "DATEOFINITIALPATHOLOGICDIAGNOSIS"
 [9] "HISTOLOGICALTYPE"                 "DISTANT.METASTASIS"              
[11] "LYMPH.NODE.METASTASIS"            "COMPLETENESS.OF.RESECTION"       
[13] "NUMBER.OF.LYMPH.NODES"            "TUMOR.STAGECODE"                 
[15] "NEOPLASM.DISEASESTAGE"            "BATCHNUMBER"                     

Input Data has 16 rows and 153 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 
          31          395          424           60           91          731 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
          31          395         1065          942           31           62 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
          28         1339          365           31          700           31 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
         458          731           62          395          485          820 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
         303          974         1004           91          881          378 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
         605          594          396          536          532          729 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
         244          530          229          447          356          182 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
         907         1096          737          788          782          724 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
        1061          783          849         1195         1153          842 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
        1403          834          790          567          397         1272 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
         724          910          519          821         1490         1860 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 
         295          289          285          233          175          170 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
         191            9          169           64          131          167 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
         258           79           52           70          217          526 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-FC-7708 TCGA-G9-6329 TCGA-G9-6332 
          43          284          187           32          923         2328 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6348 
        1925         1669         1649         1338          554         1144 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
        1215          847         1000         1008          822          993 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
         841          804          101          875          851          806 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 
         846          505          518          664          390          356 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
        1442         1014         1109          674          457          486 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-HC-7075 TCGA-HC-7077 
         451          324          512           31           61           NA 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7209 TCGA-HC-7211 TCGA-HC-7212 
         162           89           61           31           30           31 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 
          60           51           72           30           63           53 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
          45           51           57           62           61           34 
TCGA-HC-7752 TCGA-HC-7818 TCGA-HC-7821 TCGA-HC-8265 TCGA-HI-7168 TCGA-HI-7169 
          98           45           56           62         2315         1949 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
        1899           NA           98 
Variable 1:'AGE':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=129,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=TRUE.
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=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'DISTANT.METASTASIS':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'LYMPH.NODE.METASTASIS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'COMPLETENESS.OF.RESECTION':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                       "LYMPH.NODE.METASTASIS"    
[3] "COMPLETENESS.OF.RESECTION" "NUMBER.OF.LYMPH.NODES"    
[5] "TUMOR.STAGECODE"          
[1] "TUMOR.?STAGE" "5"           
[1] "stage2"
vv
T2A T2B T2C T3A T3B  T4 
  5   1  60  56  25   5 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 153 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=27, binary=FALSE, numeric=TRUE
LYNX1 
10168 
LYMPH.NODE.METASTASIS, nv=2, binary=FALSE, numeric=FALSE
DYRK2 
 5271 
COMPLETENESS.OF.RESECTION, nv=3, binary=FALSE, numeric=FALSE
WHAMM 
19120 
NUMBER.OF.LYMPH.NODES, nv=9, binary=FALSE, numeric=TRUE
ERP29__1 
    5692 
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
[1] "Clinical variable TUMOR.STAGECODE has too few non-missing values, n=0"
> q(save="no")
