
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/OV/1709129/0.GDAC_RPPA_preprocess.Finished/OV.rppa.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/OV/1709128/1.GDAC_clinicalDataPicker.Finished/OV.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=580, in expression file=412, common to both=407
Number of genes in original expression dataset=165
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                                      
 [2] "DAYSTODEATH"                                       
 [3] "DAYSTOLASTFOLLOWUP"                                
 [4] "VITALSTATUS"                                       
 [5] "DCCUPLOADDATE"                                     
 [6] "PRIMARYSITEOFDESEASE"                              
 [7] "GENDER"                                            
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"                  
 [9] "RADIATIONTHERAPY"                                  
[10] "KARNOFSKYPERFORMANCESCORE"                         
[11] "EXAMINATIONS.EXAMINATION.KARNOFSKYPERFORMANCESCORE"
[12] "HISTOLOGICALTYPE"                                  
[13] "TUMORGRADE"                                        
[14] "TUMORSTAGE"                                        
[15] "PATIENTTUMORRECURRENCESTATUS"                      
[16] "DAYSTOTUMORRECURRENCE"                             
[17] "CHEMOTHERAPY"                                      
[18] "RADIATIONS.RADIATION.REGIMENINDICATION"            
[19] "NEOADJUVANTTHERAPY"                                
[20] "BATCHNUMBER"                                       

Input Data has 20 rows and 407 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
          55         1495         1418           NA          563          361 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1356 TCGA-04-1357 TCGA-04-1360 TCGA-04-1361 
        1483          656         1499           NA           NA          989 
TCGA-04-1362 TCGA-04-1369 TCGA-04-1370 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 
        1348          642         1824         1720         1265          608 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
          NA         1167         2561         1685         1487          848 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-09-1662 TCGA-09-1664 
         871         1966         1102         1451         2717         2278 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 TCGA-09-2043 
        1265         1751          547           92          260          187 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2051 TCGA-09-2054 TCGA-09-2055 
         186         1069         3418         1919          636          819 
TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0931 TCGA-10-0933 TCGA-10-0936 
         379         1652          788          982          356         1089 
TCGA-13-0720 TCGA-13-0725 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 
        1355          377          873          923          265          237 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0884 TCGA-13-0886 
         247          252          249         1073         3260         2259 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0891 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 
        2027         2141         2099         1509         1748         1708 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0913 
         589         1441         1367         1128          842          912 
TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 
         643          420          141          201          224          180 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
         208          143          128          162         1661         2648 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 
        1877          894         2982          681         2154         2521 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 
        1595         2237         1161         1497          129         1144 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
        1167          425          999          504          128          134 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 
         145          126          118           94          372          261 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 
         328          266          295          836          772          580 
TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
         507           89           81         1562         1658           98 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 
         194         1189         1018         1768           16         3525 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 
        2661         2788         2342           84          143          137 
TCGA-23-2647 TCGA-23-2649 TCGA-24-0966 TCGA-24-0970 TCGA-24-0979 TCGA-24-0980 
         135          116          232          354         1264          233 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 
         679         1645         1933         1442          194          238 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1427 TCGA-24-1428 
         239           23          190          183          146          528 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 
         862          583          568         1324          260         2218 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 
         379         1373         3224          277          104           36 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 
         675          820         1745         1955          493         1721 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
        1249         1579         1259         1767         2692         2148 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
        1213          594         1341         1384         1451          787 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
         312          524         2742         2687         1470         1163 
TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1849 TCGA-24-1850 
         253          113          116          133          175          167 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 TCGA-24-2020 
         298          689          919          499         2467         4623 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
        1364         1769         1059         3336          439         1641 
TCGA-24-2033 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
         562         1947         1353         1736         1100           24 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
          11         1446          962         1356           25         2049 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 
        1102          506         1007         1699         1620           31 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1318 TCGA-25-1319 
         819          973         1553         1126         1064         1977 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1325 TCGA-25-1326 
        1124         1033           91          365          976          944 
TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
        1979           90          565          548          480           11 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 
         626          239            9         1732         1843         1558 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2390 TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 
        2587          396           NA         1492         1157           92 
TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 
         365         1369          608         1278           90          882 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 
         942          820         2399         1360         1435         3095 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
        1172           24         1025          948         2077           16 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 
         514          567         1815          555         1276         1053 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 
         517         2606         1914         1189          950          699 
TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 
         741          685          526          376          360          374 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 TCGA-29-2425 TCGA-29-2427 
         454          254          219         1053         1977         1900 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2435 
        1372          148         1285          360          349           34 
TCGA-29-2436 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 
         297         1579           75          477         1462         1366 
TCGA-30-1861 TCGA-30-1869 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
        1058         1563          738          914         1484         1386 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1955 TCGA-36-1568 TCGA-36-1569 
         918          571          683         1293          874          884 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 
         655          695          260          914          783          847 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2533 
         737          751         1066         1004          897           NA 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 
         906          788          763          724          657           68 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
         638          557          624          431          184          491 
TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
         349          435          276          287          230          227 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1586 TCGA-59-2348 TCGA-59-2349 TCGA-59-2351 
         232           NA          679         5480         2437         3532 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 
         286         1046          164         1362          338          245 
TCGA-61-1724 TCGA-61-1727 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
         637          564          132          966          866         1484 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 
        1089           74         1024         1329           43          256 
TCGA-61-1900 TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 
         176          396         1038          952         1126         1292 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 
        1488         1721         2060          479         1161           60 
TCGA-61-2000 TCGA-61-2003 TCGA-61-2009 TCGA-61-2012 TCGA-61-2017 TCGA-61-2018 
         441          121         1212          932         1398         1381 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
         146          145         1573         2182         1875         1776 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2111 
        1992         1688          197         2337          629         3824 
TCGA-61-2113 TCGA-61-2610 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
         676         1579          193          945          261 
Variable 1:'AGE':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=200,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=360,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'EXAMINATIONS.EXAMINATION.KARNOFSKYPERFORMANCESCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'TUMOR.GRADE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'TUMOR.STAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'PATIENTTUMORRECURRENCESTATUS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'DAYSTOTUMORRECURRENCE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'CHEMOTHERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 19:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                         "PRIMARY.SITE.OF.DISEASE"    
[3] "KARNOFSKY.PERFORMANCE.SCORE" "TUMOR.STAGE"                
[5] "NEOADJUVANT.THERAPY"        
[1] "TUMOR.?STAGE" "4"           
[1] "stage2"
vv
  1   2   3   4 
 14  19 317  52 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 407 columns, 1 survival variables, and 5 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
MAPK1 MAPK3|MAPK_PT202_Y204-R-V 
                             81 
AGE, nv=55, binary=FALSE, numeric=TRUE
PGR|PR-R-V 
       101 
PRIMARY.SITE.OF.DISEASE, nv=3, binary=FALSE, numeric=FALSE
CDH1|E-CADHERIN-R-V 
                 50 
KARNOFSKY.PERFORMANCE.SCORE, nv=4, binary=FALSE, numeric=TRUE
ANXA1|ANNEXIN_I-R-V 
                 19 
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "num to class table"
vv1
 40  60  80 100 
  1  14  33   3 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
PEA15|PEA-15-R-V 
             107 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
     14      19     317      52 
NEOADJUVANT.THERAPY, nv=2, binary=FALSE, numeric=FALSE
EIF4EBP1|4E-BP1-R-V 
                  2 
> q(save="no")
