
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/mRNAseq_preprocessor/OV/1676928/0.mRNAseq_preprocessor.Finished/OV.mRNAseq_RPKM_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/OV/1669672/1.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=297, common to both=297
Number of genes in original expression dataset=18892
[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 297 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-04-1348 TCGA-04-1357 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1514 
        1483           NA         1348         1024         2328         1720 
TCGA-04-1519 TCGA-09-0364 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 
          NA          887         1756          546         1081          303 
TCGA-09-1662 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 
        2717         1751         1882         1684          927          547 
TCGA-09-1673 TCGA-09-1674 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2051 
          92          260          186         1069          137         1919 
TCGA-09-2054 TCGA-09-2056 TCGA-10-0928 TCGA-10-0936 TCGA-13-0730 TCGA-13-0799 
         636          379          562         1089          541          237 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0883 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 
         247          252         2096         2068         1319         1748 
TCGA-13-0899 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0924 TCGA-13-1403 
        1708          912          643          420          185          331 
TCGA-13-1405 TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 TCGA-13-1489 TCGA-13-1497 
         224          143          128         2648         2521         1652 
TCGA-13-1498 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1511 TCGA-13-1512 
        1144          128          134          145          118           94 
TCGA-13-2060 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1687 
         261          836          772          580          507           81 
TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1029 TCGA-23-1109 TCGA-23-1111 
        1233          816          965          268         1562           98 
TCGA-23-1114 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1809 TCGA-23-2077 
        2089          130         1189         1018           16         3525 
TCGA-23-2078 TCGA-23-2081 TCGA-23-2084 TCGA-24-0975 TCGA-24-1103 TCGA-24-1413 
        2661         2342         1516          663         1645          192 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
         194          238          243          239           23          190 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1434 
         183          181          146          528          862          568 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1467 TCGA-24-1469 TCGA-24-1474 
        1324          260         2218         3224          277          675 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 
         820         1745         1955          493         1721         1249 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
        1579         1259         1767         2692         2148         1213 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1567 
         594         1341         1384         1451          787          524 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
        2742         2687         1163          253          106          113 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1924 TCGA-24-1928 
         133          343          175          167          919          336 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 
        2467          148         4623         1364         1769         1059 
TCGA-24-2027 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 
        3336          562          857         1947         1353         1736 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 
          24           11         1446          962         1356           25 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 
        2049         1102          506         1699         1620           31 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
         819          973         1553         1126           31         1064 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1324 
        1977         1124         1033           91          365         1035 
TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 
         944         1979           90          565          548          480 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
          11          626          239            9         1732         1843 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-2042 TCGA-25-2391 
        1081         1558          454          760          396         1492 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
          31         1157           92          365         1369          608 
TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
        1278           90          882          820         2399         1360 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 
        1435         3095         1172           24         1025          948 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
        2077           16          514          567         1815          555 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1770 
         889         1053          517         2606         2031          741 
TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 
         360          454          254          219          163         1053 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-30-1718 TCGA-30-1855 
        2621         1977         1900         1372         1579           75 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1891 TCGA-31-1944 TCGA-31-1946 
        1366         1058          185          914         1386          918 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 
         571          683          204         1341           66          874 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 
         884          655          695          686          260          914 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-57-1582 TCGA-57-1583 
         783          847          737          751          731          346 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2350 
         643           53          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-61-1900 TCGA-61-1907 
        1089           74         1024         1329          176          952 
TCGA-61-1910 TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 
        1126         1721         1321          479         1161           60 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 
         168          441          547          121          931         1212 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
         932           36          145         1573         2182         1875 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
        1844         1992         1688          197         2337          629 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
        1354         3824          676 
Variable 1:'AGE':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=163,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=265,	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=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
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=3,	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=TRUE.
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"                         "KARNOFSKY.PERFORMANCE.SCORE"
[3] "TUMOR.STAGE"                 "NEOADJUVANT.THERAPY"        
[1] "TUMOR.?STAGE" "3"           
[1] "stage2"
vv
  2   3   4 
 18 241  36 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 297 columns, 1 survival variables, and 4 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
GMPPB|29925_CALCULATED 
                 12605 
AGE, nv=48, binary=FALSE, numeric=TRUE
C8ORF55|51337_CALCULATED 
                   16844 
KARNOFSKY.PERFORMANCE.SCORE, nv=3, binary=FALSE, numeric=TRUE
EXOC3|11336_CALCULATED 
                 14212 
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "num to class table"
vv1
 60  80 100 
  5   9   2 
TUMOR.STAGE, nv=3, binary=FALSE, numeric=TRUE
BACE1|23621_CALCULATED 
                  2772 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 2 Stage 3 Stage 4 
     18     241      36 
NEOADJUVANT.THERAPY, nv=2, binary=FALSE, numeric=FALSE
CRIM1|51232_CALCULATED 
                 10113 
> q(save="no")
