
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/miRseq_preprocessor/PRAD-TP/4428936/0.miRseq_preprocessor.Finished/PRAD-TP.miRseq_RPKM_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/PRAD-TP/4401844/PRAD-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=166, in expression file=232, common to both=164
Number of genes in original expression dataset=470
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                     "VITALSTATUS"                     
 [3] "DAYSTODEATH"                      "DAYSTOLASTFOLLOWUP"              
 [5] "PRIMARYSITEOFDESEASE"             "NEOPLASM.DISEASESTAGE"           
 [7] "PATHOLOGY.T.STAGE"                "PATHOLOGY.N.STAGE"               
 [9] "PATHOLOGY.M.STAGE"                "DCCUPLOADDATE"                   
[11] "GENDER"                           "DATEOFINITIALPATHOLOGICDIAGNOSIS"
[13] "RADIATIONTHERAPY"                 "HISTOLOGICALTYPE"                
[15] "COMPLETENESS.OF.RESECTION"        "NUMBER.OF.LYMPH.NODES"           
[17] "BATCHNUMBER"                     

Input Data has 17 rows and 164 columns.

[1] "Batch" "17"   
[1] "Last Follow UP"
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
          91          212          671           31          395          424 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 
          60           91          731           31          395          942 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
          31           62           28         1339          365           31 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
         700           31          458          731           62          395 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
         485          820          303          974         1004           91 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
         881          378          605          594          396          536 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
         532          729          244          530          229          447 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
         356          182          907         1096          737          788 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
         782          724         1061          783          849         1195 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
        1153          842         1403          834          790          567 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
         397         1272          724          910          519          821 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7321 
        1490         1860          295          289          285          233 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
         175          170          191            9          169           64 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
         131          167          258           79           52           70 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8469 
         217          526           43          284          187         1946 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-A46B TCGA-FC-7708 TCGA-FC-7961 TCGA-G9-6329 
         821           NA          162           32           70          923 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6342 TCGA-G9-6343 
        2328         1925         1669         1649         1338          554 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
        1144         1215          847         1000         1008          822 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
         993          841          804          101          875          851 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 
         806          846          505          518          664          390 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 
         356         1442         1014         1109          674          457 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-HC-7075 
         486          451          324          512           31           61 
TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7209 TCGA-HC-7211 
          NA          162           89           61           31           30 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7736 TCGA-HC-7737 
          31           60           51           72           30           63 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
          53           45           51           57           62           61 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7821 TCGA-HC-8265 
          34           98           32           45           56           62 
TCGA-HC-A4ZV TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
          23         2391         1949         1899           NA           98 
TCGA-J4-8200 TCGA-J4-A67N 
         196          502 
Variable 1:'AGE':	nDistinctValues=29,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=TRUE.
Variable 3:'DAYSTODEATH':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=134,	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=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
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:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'COMPLETENESS.OF.RESECTION':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'BATCH.NUMBER':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                       "PATHOLOGY.T.STAGE"        
[3] "PATHOLOGY.N.STAGE"         "COMPLETENESS.OF.RESECTION"
[5] "NUMBER.OF.LYMPH.NODES"    
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "2"          
[1] "PATHOLOGY.N" "3"          
Output Data has 164 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=29, binary=FALSE, numeric=TRUE
HSA-MIR-495 
        348 
PATHOLOGY.T.STAGE, nv=3, binary=FALSE, numeric=TRUE
HSA-MIR-30A 
        205 
[1] "PATHOLOGY.T.STAGE"
[1] "num to class table"
vv1
 2  3  4 
70 89  4 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
HSA-MIR-1271 
          51 
COMPLETENESS.OF.RESECTION, nv=3, binary=FALSE, numeric=FALSE
HSA-MIR-526B 
         370 
NUMBER.OF.LYMPH.NODES, nv=9, binary=FALSE, numeric=TRUE
HSA-MIR-378 
        296 
> q(save="no")
