
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/miRseq_preprocessor/OV/2008721/0.miRseq_preprocessor.Finished/OV.miRseq_RPKM_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/OV/1971866/1.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=454, common to both=454
Number of genes in original expression dataset=415
[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 454 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 
        1224         1247         1495           61           NA          563 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 
        1992         1918         1483          656         1946         1499 
TCGA-04-1357 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
          NA          989         1348         1024         2328         2174 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 
        1720          608           NA         1167         3622          884 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
        2561         1685          848          871         1966         1102 
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0366 TCGA-09-1661 
         969         1451         1379          887         1756         1169 
TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 
        2717         1265         1751         1882         1684          927 
TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
         547           92          260          186         1069          137 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2056 TCGA-10-0926 
        2163         1919         1209          636          379          788 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0933 TCGA-10-0934 TCGA-13-0714 TCGA-13-0720 
        2478          562          356          118          189         1355 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0760 
        1204           83         1678           75          340          351 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0797 TCGA-13-0799 
         651          256         1184         1117          265          237 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 TCGA-13-0883 
         247          252          249         1333         1073         2096 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
        3260         2780         2259         2027         2141         1880 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0900 TCGA-13-0901 
        2068         2099         1319         1509         1736          589 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
        1441         1470         1455         1367         1364         1128 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
         842         1036          912          643          453          420 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
         141          195          185          331          201          224 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
         184          180          208          143          128          162 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 
        1661         2648         1877          894         2982          629 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
         681         2154         2521         1595         2237         1161 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
        1497          129         1652         1144         1167          425 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
         999          504          128          134          145          126 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2060 TCGA-20-0987 TCGA-20-0990 
          78          118           94          261          701          789 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
         797          836          772          580          507           89 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 
          81         1446         1293         1233          816          965 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1032 TCGA-23-1107 TCGA-23-1109 
        1503          268          885           68            9         1562 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1118 TCGA-23-1119 
        1658           98          949         2089         2616         3953 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 
         130          194         1189         1018         1768           16 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 
         759         3525         2661         2788         2342         1516 
TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 
         232          597          354          663         1264          679 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
        1645         1933         1442          192          194          238 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
         243          239           23          190          183          181 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 
         163          146          528          862          583          568 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 
        1324          260         2218          379         1373         3224 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
         277          104           36          675          820         1745 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
        1955          493         1721         1249         1579         1259 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
        1767         2692         2148         1213          594         1341 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
        1384         1451          787          312          524         2742 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
        2687         1470         1163          253          106          113 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 
         116          133          343          175          167          298 
TCGA-24-1923 TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
         689          919          336         2467          148         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-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 
         562          857         1947         1353         1736         1100 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 
          24           11         1446          962         2143         1356 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 
          25         2049         1102          506         1699         1620 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
          31          819          973         1553         1126           31 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
        1064         1977         1124         1033           91          365 
TCGA-25-1324 TCGA-25-1325 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 
        1035          976          944         1979           90          565 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
         548          480           11          626          239            9 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
        1732         1843         1081         1558          454          760 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 
         549         2587          396         1492           31         1157 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 
          92          365         1369          608         1278           90 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 
         882          942          820         2399         1360         1435 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
        3095         1172           24         1025          948         2077 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
          16          514          567         1815          555         1276 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 
         889         1053          517         2606         2031         1914 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
        1189          950          699          741          685          526 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
         360          374          454          254          219          163 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-30-1714 
        1053         2621         1977         1900         1372         1158 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 
        1579         1103           75          477            8         1462 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 
        1366         1058          185         1114           36         1751 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
         738          914         1484         1386          918          571 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
         683          204         1341           66          874          884 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 
         655          695          686          260          914          783 
TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
         847          737          751          731          346          643 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2350 
          53          679          762          761         5480          679 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 
        3532          286         1046           65          164          338 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1728 TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 
         637          955          848          966         1484         1364 
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-61-1901 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 
         176          347         1038          952         1126         1292 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 
        1488         1721         2060         1321          479         1161 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 
          60          168          441          547          121          931 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
        1212          932           36          145         1573         2182 
TCGA-61-2095 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
        1875         1844         1992         1688          197         2337 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
         629         1354         3824          676 
Variable 1:'AGE':	nDistinctValues=53,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=235,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=396,	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=7,	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=FALSE.
Variable 19:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "PRIMARY.SITE.OF.DISEASE"               
[3] "KARNOFSKY.PERFORMANCE.SCORE"           
[4] "TUMOR.STAGE"                           
[5] "RADIATIONS.RADIATION.REGIMENINDICATION"
[6] "NEOADJUVANT.THERAPY"                   
[1] "TUMOR.?STAGE" "4"           
[1] "stage2"
vv
  2   3   4 
 24 352  74 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 454 columns, 1 survival variables, and 6 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
HSA-MIR-135B 
          89 
AGE, nv=53, binary=FALSE, numeric=TRUE
HSA-MIR-1269 
          53 
PRIMARY.SITE.OF.DISEASE, nv=3, binary=FALSE, numeric=FALSE
HSA-MIR-632 
        359 
KARNOFSKY.PERFORMANCE.SCORE, nv=4, binary=FALSE, numeric=TRUE
HSA-MIR-141 
         94 
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "num to class table"
vv1
 40  60  80 100 
  2  17  39   6 
TUMOR.STAGE, nv=3, binary=FALSE, numeric=TRUE
HSA-MIR-1978 
         155 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 2 Stage 3 Stage 4 
     24     352      74 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-34A 
        240 
NEOADJUVANT.THERAPY, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-665 
        374 
> q(save="no")
