
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/LGG-TP/4402970/LGG-TP.rppa.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/LGG-TP/4397071/LGG-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=243, in expression file=258, common to both=222
Number of genes in original expression dataset=189
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "DCCUPLOADDATE"                         
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "RADIATIONTHERAPY"                      
[11] "KARNOFSKYPERFORMANCESCORE"             
[12] "HISTOLOGICALTYPE"                      
[13] "RADIATIONS.RADIATION.REGIMENINDICATION"
[14] "BATCHNUMBER"                           

Input Data has 14 rows and 222 columns.

[1] "Batch" "14"   
[1] "Last Follow UP"
TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 TCGA-CS-5393 
         143           NA          552          323         1966         1222 
TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6665 
           3          303           NA           NA          725          378 
TCGA-CS-6666 TCGA-CS-6668 TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 
         257          243          224          200         2977         1809 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 
        1726         1458         1594         1419         1526         1354 
TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC 
         404         1614          915          313          387          840 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DH-5140 
         822          572          559         2219          383           NA 
TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 TCGA-DU-5847 TCGA-DU-5849 
         968          921          438          244          547          442 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 
         530           NA          407          257          207         5546 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 
         576          531          460         6423         1585          682 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 
        1491         2286         1401           NA           37         2660 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
         213           NA           NA          605           NA           NA 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
        3469          242          234           NA           NA         4752 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
        4205           NA           NA           NA           NA           NA 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
        2761           NA          800           NA           NA         2868 
TCGA-DU-7298 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
          NA           NA           NA         1834           NA         1277 
TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 
          84           NA           NA          121          197          201 
TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TY TCGA-E1-5302 
         184           67           97          107          371         1525 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
        2051         1251         2432         1762         4084         2378 
TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 
        2907         3978          160         1099          547          377 
TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 
         979          570          453          391          382          467 
TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 
         124         1020          233          313          293          105 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 
         100           69          121          215           96          361 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MY TCGA-FG-A60J TCGA-HT-7467 
         199          744           18          294          214            3 
TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 
         203          238          268            4            1          503 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 
         114          530          199          194          216         2287 
TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 
        1800         1826         4687          121          153          907 
TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 
         705         3283          139          526           NA          671 
TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 
        1399         1706           NA          434            5          494 
TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 
          23         1359          184         1300            3          964 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 
         454            3            3           90          533          210 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 
         442          292          585         1189            7         1540 
TCGA-HT-7860 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
          15         1130           10            4          112          162 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 TCGA-HT-8012 
          89           51          955           50          494          286 
TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8106 
          NA          654         1004          372          190            3 
TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 
          14          120          142            7          900          118 
TCGA-HT-8558 TCGA-HT-8564 TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 
          52          477          608          409          141          165 
TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 TCGA-IK-7675 TCGA-IK-8125 TCGA-P5-A5EW 
         854          285           13           NA         1120          204 
Variable 1:'AGE':	nDistinctValues=54,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=175,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'BATCH.NUMBER':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "KARNOFSKY.PERFORMANCE.SCORE"           
[4] "HISTOLOGICAL.TYPE"                     
[5] "RADIATIONS.RADIATION.REGIMENINDICATION"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 222 columns, 1 survival variables, and 5 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
ANXA1|ANNEXIN-1-M-E 
                 23 
AGE, nv=54, binary=FALSE, numeric=TRUE
IGFBP2|IGFBP2-R-V 
               83 
GENDER, nv=2, binary=FALSE, numeric=FALSE
RAB11A RAB11B|RAB11-R-E 
                    125 
KARNOFSKY.PERFORMANCE.SCORE, nv=6, binary=FALSE, numeric=TRUE
IGFBP2|IGFBP2-R-V 
               83 
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
SYK|SYK-M-V 
        148 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
CTNNA1|ALPHA-CATENIN-M-V 
                     165 
> q(save="no")
