
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.11.3544/ClinicalAnalysisAllGenes.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ClinicalAnalysisAllGenes_new.11.3544/", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBM-TP/2328053/2.GDAC_MergeDataFiles.Finished/GBM-TP.mirna__h_mirna_8x15k__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/GBM-TP/2330191/1.GDAC_clinicalDataPicker.Finished/GBM-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=565, in expression file=491, common to both=482
Number of genes in original expression dataset=534
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "KARNOFSKYPERFORMANCESCORE"             
[10] "HISTOLOGICALTYPE"                      
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "BATCHNUMBER"                           

Input Data has 12 rows and 482 columns.

[1] "Batch" "12"   
[1] "Last Follow UP"
TCGA-02-0001 TCGA-02-0003 TCGA-02-0004 TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 
         278          144          345          558          705          322 
TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0021 
        1077          630         2511          627         1699         2361 
TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 
         612         1614         1300          748          315         2755 
TCGA-02-0033 TCGA-02-0034 TCGA-02-0037 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 
          86          430          109          326          320          556 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0055 
         447           97          458          383          199           76 
TCGA-02-0057 TCGA-02-0058 TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 
         604          254          291          183          600          804 
TCGA-02-0069 TCGA-02-0070 TCGA-02-0071 TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 
         873          762          167          310          634          828 
TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0085 TCGA-02-0086 TCGA-02-0087 
        2729          691            7         1560          268         1757 
TCGA-02-0089 TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0106 TCGA-02-0107 
         515          106          821         1977          355          537 
TCGA-02-0111 TCGA-02-0113 TCGA-02-0114 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
         704         2817         3040          476         1489          503 
TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 
         514          538          327          440          121          422 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
         432          485          372          300          234          323 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0333 TCGA-02-0337 TCGA-02-0338 
           5          484          782          133          764          322 
TCGA-02-0339 TCGA-02-0422 TCGA-02-0430 TCGA-02-0432 TCGA-02-0439 TCGA-02-0440 
         377          441          321         1433           20          345 
TCGA-02-0446 TCGA-02-0451 TCGA-02-0456 TCGA-02-2466 TCGA-02-2470 TCGA-02-2483 
         281          492          102          511          393          465 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 
         469          492            8          123         1439            3 
TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0133 TCGA-06-0137 
         108          691          988          320          428          701 
TCGA-06-0138 TCGA-06-0139 TCGA-06-0141 TCGA-06-0143 TCGA-06-0145 TCGA-06-0146 
         674          327          280          357           71          611 
TCGA-06-0147 TCGA-06-0149 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0156 
         508          238          359          389          263          164 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 
          97          166           78         1729          161          579 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0176 
          95          396            7           67           83         1561 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 
          60         1642          578           77         1228         1126 
TCGA-06-0187 TCGA-06-0188 TCGA-06-0189 TCGA-06-0190 TCGA-06-0192 TCGA-06-0194 
         801          866          454          313          556          142 
TCGA-06-0195 TCGA-06-0197 TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 
         214           79          166          151          360            6 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 
         378          684           10          548          314          359 
TCGA-06-0241 TCGA-06-0394 TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0410 
         455          313          168            8         2145          142 
TCGA-06-0412 TCGA-06-0413 TCGA-06-0414 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
         245            5         1065          375           98          136 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
         293           62          285          678          594          163 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0877 
          82           65           28          279          271          204 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
         218          699          178          165          637          226 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1805 
         193          109          815          263          239          127 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
          33           23          149          282           86          259 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
         181          207          182          133           13          285 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5417 TCGA-06-5418 TCGA-08-0244 
         273          260          204          155           83          690 
TCGA-08-0245 TCGA-08-0246 TCGA-08-0344 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
        1057          119         3310           53          132          419 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 TCGA-08-0352 TCGA-08-0353 
         316          231          103         1636           39          195 
TCGA-08-0354 TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 
         458          685          447         1084          593           29 
TCGA-08-0360 TCGA-08-0373 TCGA-08-0375 TCGA-08-0380 TCGA-08-0385 TCGA-08-0386 
         352          134          279          330           31          478 
TCGA-08-0389 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0511 
          97          322            9           17          106          235 
TCGA-08-0512 TCGA-08-0514 TCGA-08-0516 TCGA-08-0517 TCGA-08-0518 TCGA-08-0520 
         358          259          561         1770           39          326 
TCGA-08-0521 TCGA-08-0522 TCGA-08-0524 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 
         146          555          198          486          526          168 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 
         438           49          316          181          218         2004 
TCGA-12-0657 TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 
           3         1161          790          734          185           80 
TCGA-12-0703 TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 
         550           NA          378         1615         1311          167 
TCGA-12-0776 TCGA-12-0778 TCGA-12-0780 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
         277          451          434          562          323          715 
TCGA-12-0826 TCGA-12-0827 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 
         845         1179          271          626         3880          177 
TCGA-12-1090 TCGA-12-1091 TCGA-12-1092 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 
         189          929          658          364          346          482 
TCGA-12-1096 TCGA-12-1097 TCGA-12-1098 TCGA-12-1099 TCGA-12-1597 TCGA-12-1598 
         277          442          121          103          427          287 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
         769          414          194         1807         1314          784 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
         351          333          358         1050          357          398 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0783 TCGA-14-0786 TCGA-14-0787 
          98           61          459          188          701           68 
TCGA-14-0789 TCGA-14-0790 TCGA-14-0812 TCGA-14-0813 TCGA-14-0817 TCGA-14-0865 
         342          418           99           41          164          502 
TCGA-14-0866 TCGA-14-0867 TCGA-14-0871 TCGA-14-1034 TCGA-14-1037 TCGA-14-1396 
         801           62          879          485          587           34 
TCGA-14-1401 TCGA-14-1402 TCGA-14-1451 TCGA-14-1452 TCGA-14-1453 TCGA-14-1454 
         114          974          703          216           35          917 
TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
          28         1245          186          378           30           59 
TCGA-14-1821 TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
         540          542          232          179          217          532 
TCGA-14-2555 TCGA-14-3476 TCGA-14-3477 TCGA-14-4157 TCGA-15-0742 TCGA-15-1446 
         242           12          114          103          300          581 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0848 TCGA-16-0849 TCGA-16-0850 
        1618          167          119          302          793          496 
TCGA-16-0861 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 TCGA-16-1060 
         130          882           25          301          406          111 
TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0955 TCGA-19-0957 TCGA-19-0960 
         556          425          195          358          665          262 
TCGA-19-0962 TCGA-19-0963 TCGA-19-0964 TCGA-19-1385 TCGA-19-1386 TCGA-19-1387 
          13          434          103          327          276          181 
TCGA-19-1388 TCGA-19-1389 TCGA-19-1390 TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 
         394          141          772          106          217          385 
TCGA-19-1788 TCGA-19-1789 TCGA-19-1790 TCGA-19-1791 TCGA-19-2619 TCGA-19-2620 
         111           99          153            4          294          148 
TCGA-19-2621 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
          33          229            5          124          501          213 
TCGA-19-4068 TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 
         136          305          422          296          216          285 
TCGA-26-5132 TCGA-26-5133 TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 
         286          452          167          269           37           48 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
         146          504           NA          555         1008          648 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
         914          427          350          752          316          316 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1745 
         489          231           87          438          479          344 
TCGA-28-1746 TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 
           6           77          279          253          231          257 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1756 TCGA-28-1757 TCGA-28-1760 TCGA-28-2502 
          36           46           86            4          143           20 
TCGA-28-2506 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
         205          145          222          160          119          275 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
         473           77          298          432          237          415 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-32-1970 TCGA-32-1973 TCGA-32-1976 
         128          259          319          467          641           15 
TCGA-32-1977 TCGA-32-1978 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-1991 
           3          482          142          386          451          515 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2616 TCGA-32-2632 
         372          632          456          485          223          269 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 
         270          224          400          338          112          383 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
         356          330          165           26          406          272 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-76-4925 
         290           30          135          183            6          145 
TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 
         138          535           94          111          278         1458 
TCGA-76-4934 TCGA-76-4935 
          77          328 
Variable 1:'AGE':	nDistinctValues=72,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=308,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=367,	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=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'BATCH.NUMBER':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "KARNOFSKY.PERFORMANCE.SCORE"           
[4] "RADIATIONS.RADIATION.REGIMENINDICATION"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 482 columns, 1 survival variables, and 4 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
HSA-MIR-222 
        172 
AGE, nv=72, binary=FALSE, numeric=TRUE
HSA-MIR-148A 
          97 
GENDER, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-361 
        230 
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
HSA-MIR-189 
        125 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
KSHV-MIR-K12-4-3P 
              526 
> q(save="no")
