
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/UCEC/2009125/0.miRseq_preprocessor.Finished/UCEC.miRseq_RPKM_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/UCEC/1972821/1.GDAC_clinicalDataPicker.Finished/UCEC.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=451, in expression file=485, common to both=436
Number of genes in original expression dataset=564
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "HISTOLOGICALTYPE"                      
[11] "TUMORGRADE"                            
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "NEOADJUVANTTHERAPY"                    
[14] "BATCHNUMBER"                           

Input Data has 14 rows and 436 columns.

[1] "Batch" "14"   
[1] "Last Follow UP"
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
          NA         4053         1079          790         2165           NA 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
          97         2717         2516         1671         1750         1447 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
        1448         1087         1167          780          495          485 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
         385          924          369           40          125          294 
TCGA-A5-A0RA TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
         555          128          927          177          241          348 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
         292          243         2768         1409           NA          161 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK 
         156          223          230           31           60           12 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
          49           31           61           91           15           34 
TCGA-AJ-A3BG TCGA-AJ-A3BH TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
          31           NA           61           51           NA           64 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE 
          65           50           39           28          210           78 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AP-A051 
          41           52           NA           59          142         2545 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A059 TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
         181           NA          250          371          260           NA 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
        3443         2906         2986          103         1921           NA 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP 
        2602          965         2141          825         1992         1875 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
        1906         1668         1185          385         1816         1650 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
        1329          952           NA         1184         1131          204 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S 
         691          317          523          267           17           NA 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
         603          902         2078         2191         1413         1075 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
        1398         2024         1639           NA         1554          833 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
         913         1479         1065          868         1148         1333 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
        1219         2004          404          584          515          412 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
         464          617          378          610         2337         2207 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 
        1645         2052          764         1107          337           NA 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
          NA         2167         1020         1861         2090         1016 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
        1232          489          660          539          831           NA 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
          NA         1176            7            3           10            4 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G8 
           6           NA            1            4           NA           36 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0JT 
         254          440            4         2068         1241         1312 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
        1483         1125         1360          821          689          679 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
         746          682          700          466          426          372 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
         542          166          124          265         5279         3076 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11M TCGA-B5-A11N 
        2317         2038         1291         1396         1117         1147 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
        1034         1120          702          837          650          271 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
         231          339          337          315          291          259 
TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
        5690           NA          380          220          174           NA 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
         465          389         1890          194          252          237 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
         316          742          480          241          698          690 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MH TCGA-BG-A0MI 
         765           NA          827          896         1341           NA 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
        1021          761          553          240          231          128 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
         224          260          131          490          868          907 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
        1151          279          186          230          231          252 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
         155          169           46           14           NA           16 
TCGA-BG-A2L7 TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
         177          289          371          211          239          578 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
         202          233           NA          714         2260         2002 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
          NA         2034         1443         1514         2204           NA 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
        2606         1749         2540         1843           27           36 
TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
        2191          595          149           31         1650         1429 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
        1507         1661         1207          512           69          690 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
           8           17          147          578          350          377 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
          53           43          480         1012          915          909 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A162 TCGA-D1-A163 TCGA-D1-A165 
          NA          112          892          976          938           20 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
         478          913          905          744          908          909 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
          80           NA           NA          742          640          864 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
         221           21          238           43          111          532 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
         324          202          506          347          206           19 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
         212            1          160           39          454          429 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
         459          311           46           54           NA          326 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
          70          396           43          311           22          399 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
         396            8            2          377           32           NA 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
         107         1260           NA         1365            8           NA 
TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
         125          405         1005         1114          739          943 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ 
          NA           NA           NA         2797          711         1289 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
         427           NA          202           NA           66           46 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
         332          243          328          972         1066         1004 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EY-A1G7 
         825          929          701          672           NA           NA 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
          NA          138          248          552          532          527 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
         506          510          503          424          209          360 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
         348          340          344          284          300          259 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 
         257          260          166          339          165          109 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
         252          391          235          171          774          503 
TCGA-EY-A2OQ TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
         293         1217         1064         1034         1095           NA 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
          NA          273         2557         1795          276           NA 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-H5-A2HR 
         880          761          791           53 
Variable 1:'AGE':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=38,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=337,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=4,	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=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'TUMOR.GRADE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'BATCH.NUMBER':	nDistinctValues=28,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "HISTOLOGICAL.TYPE"                     
[3] "TUMOR.GRADE"                           
[4] "RADIATIONS.RADIATION.REGIMENINDICATION"
[5] "NEOADJUVANT.THERAPY"                   
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE" "3"           
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 436 columns, 1 survival variables, and 4 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
HSA-LET-7G 
        10 
AGE, nv=59, binary=FALSE, numeric=TRUE
HSA-MIR-424 
        378 
HISTOLOGICAL.TYPE, nv=7, binary=FALSE, numeric=FALSE
HSA-MIR-9-1 
        545 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-128-2 
           64 
NEOADJUVANT.THERAPY, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-128-2 
           64 
> q(save="no")
