
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/mRNAseq_preprocessor/STAD-TP/4403200/STAD-TP.mRNAseq_RPKM_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/STAD-TP/4434906/STAD-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=614, in expression file=273, common to both=273
Number of genes in original expression dataset=23378
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "RADIATIONTHERAPY"                      
[14] "HISTOLOGICALTYPE"                      
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "COMPLETENESS.OF.RESECTION"             
[17] "NUMBER.OF.LYMPH.NODES"                 
[18] "BATCHNUMBER"                           

Input Data has 18 rows and 273 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
         171            3           NA           NA           NA           NA 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4292 TCGA-BR-4294 TCGA-BR-4357 TCGA-BR-4361 TCGA-BR-4362 TCGA-BR-4366 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4367 TCGA-BR-4368 TCGA-BR-4369 TCGA-BR-4370 TCGA-BR-4371 TCGA-BR-6452 
          NA           NA           NA           NA           NA          257 
TCGA-BR-6453 TCGA-BR-6454 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
          NA           NA          399           NA          356          212 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
         330          286           19          378          420           66 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
         353           37           20           34           23           20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
           8           37           45           14            4           32 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
          25           21            5          138           30           29 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
          21            5           33           34           25           40 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
          21           29           15           14           22           13 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
           8           36           23           12           11           10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
          67           90           17           33           42           25 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
          11           18           26           21            8           13 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
          21           25           21            9           30           21 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8677 
          23           58           65            6            6           15 
TCGA-BR-8678 TCGA-BR-8679 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
           5            5           24           50           18           17 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CR TCGA-BR-A4CS 
          19           13           20           92           51           28 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
          18           28           12           24           NA           24 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
          16           13            4           14            7            3 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5799 
          41           NA           22           15           86           99 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
         400          401            2           NA           12            2 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
           2            3            4            5            3            3 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
           4           NA            4            3            2            4 
TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
           4            4            2            3            3            3 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
          92          822          485           NA          242          245 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4442 TCGA-CG-4443 TCGA-CG-4444 
        1644           NA           NA           NA          912         1431 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
         580           NA           NA           NA          576           NA 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4475 TCGA-CG-4476 TCGA-CG-4477 TCGA-CG-5716 
         365           NA           NA           NA           31           NA 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
          NA           31           31           NA          182           29 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5732 TCGA-CG-5734 
        2131           NA           NA           NA         1674           NA 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
         376          385          582          625          573          564 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
         566          543          406          523          312          463 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
         486          389          321          344          374          243 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
          26          118          127            6           97          159 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
         145          129          210          180          244          104 
TCGA-D7-A4Z0 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
         148          237          242          199           61           NA 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
         251           12            6           92          109           31 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-HF-7131 
          NA           NA           86           17           30           NA 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-7136 TCGA-HU-8238 TCGA-HU-8244 
          NA           NA           NA           NA           46          434 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
         347          368          323           23          462          170 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH 
         374          360          463           99          519          358 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
         650          640          273          198          190          310 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
           8           64          394          589          538          374 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
         293          270          268          834          209          108 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
         319           NA           77 
Variable 1:'AGE':	nDistinctValues=50,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=137,	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=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'HISTOLOGICAL.TYPE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=17,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL.TYPE"                     
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "COMPLETENESS.OF.RESECTION"             
[10] "NUMBER.OF.LYMPH.NODES"                 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 273 columns, 1 survival variables, and 10 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
LRRC16B|90668_CALCULATED 
                   12677 
AGE, nv=50, binary=FALSE, numeric=TRUE
TMEM240|339453_CALCULATED 
                    20821 
NEOPLASM.DISEASESTAGE, nv=11, binary=FALSE, numeric=FALSE
FMO2|2327_CALCULATED 
                8390 
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
SNTB2|6645_CALCULATED 
                19421 
[1] "PATHOLOGY.T.STAGE"
[1] "num to class table"
vv1
  1   2   3   4 
 13  69 106  76 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
ATP2B1|490_CALCULATED 
                 1973 
[1] "PATHOLOGY.N.STAGE"
[1] "num to class table"
vv1
 0  1  2  3 
91 78 47 46 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
LOC100128946|100128946_CALCULATED 
                            11592 
GENDER, nv=2, binary=FALSE, numeric=FALSE
XIST|7503_CALCULATED 
               22439 
HISTOLOGICAL.TYPE, nv=7, binary=FALSE, numeric=FALSE
GEM|2669_CALCULATED 
               8800 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
CLEC3A|10143_CALCULATED 
                   5289 
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
MIR3960|100616250_CALCULATED 
                       13553 
NUMBER.OF.LYMPH.NODES, nv=31, binary=FALSE, numeric=TRUE
BX538254|?_CALCULATED 
                 3404 
> q(save="no")
