
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/mRNAseq_preprocessor/OV-TP/2844421/OV-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/OV-TP/2844038/1.GDAC_clinicalDataPicker.Finished/OV-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=579, in expression file=261, common to both=261
Number of genes in original expression dataset=18555
[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] "COMPLETENESS.OF.RESECTION"                         
[20] "BATCHNUMBER"                                       

Input Data has 20 rows and 261 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-09-1662 
          NA          887         1756          546         1081         2717 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 
        1751         1882         1684          927          547           92 
TCGA-09-1674 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2051 TCGA-09-2054 
         260          186         1069          137         1919          636 
TCGA-09-2056 TCGA-10-0928 TCGA-10-0936 TCGA-13-0730 TCGA-13-0799 TCGA-13-0800 
         379          562         1089          541          237          247 
TCGA-13-0801 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0913 
         252         2068         1319         1748         1708          912 
TCGA-13-0916 TCGA-13-0920 TCGA-13-0924 TCGA-13-1403 TCGA-13-1405 TCGA-13-1410 
         643          420          185          331          224          143 
TCGA-13-1481 TCGA-13-1497 TCGA-13-1498 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
        2648         1652         1144          128          134          145 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2060 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 
         118           94          261          836          772          580 
TCGA-20-1685 TCGA-20-1687 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1029 
         507           81         1233          816          965          268 
TCGA-23-1109 TCGA-23-1111 TCGA-23-1114 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 
        1562           98         2089          130         1189         1018 
TCGA-23-1809 TCGA-23-2077 TCGA-23-2081 TCGA-23-2084 TCGA-24-0975 TCGA-24-1103 
          16         3525         2342         1516          663         1645 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1423 
         192          194          238          243          239          190 
TCGA-24-1424 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1436 TCGA-24-1467 
         183          146          528          862          260         3224 
TCGA-24-1469 TCGA-24-1474 TCGA-24-1544 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 
         277          675          820          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-24-1850 TCGA-24-1924 TCGA-24-1930 TCGA-24-2019 
         133          343          167          919         2467          148 
TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2033 
        4623         1364         1769         1059         3336          562 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 TCGA-24-2262 
         857         1947         1353         1736           24           11 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2290 TCGA-24-2297 
        1446          962         1356           25         1102         1699 
TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
        1620           31          819          973         1553         1126 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
          31         1064         1977         1033           91          365 
TCGA-25-1324 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
        1035          944         1979           90          565          548 
TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
          11          239            9         1732         1843         1081 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 
        1558          454          760         1492           31         1157 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 TCGA-25-2409 
          92          365          608         1278          882          820 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 
        2399         1360         1435         3095         1172           24 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
        1025          948           16          514          567         1815 
TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
         555          889         1053          517         2606         2031 
TCGA-29-1770 TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
         741          360          454          254          219          163 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-30-1718 
        1053         2621         1977         1900         1372         1579 
TCGA-30-1855 TCGA-30-1860 TCGA-30-1862 TCGA-30-1891 TCGA-31-1944 TCGA-31-1951 
          75         1366          185          914         1386          683 
TCGA-31-1953 TCGA-31-1956 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
         204         1341          874          655          695          686 
TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-57-1582 
         260          783          847          737          751          731 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2350 
         346          643          762          761         5480          679 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 TCGA-61-1724 
        3532          286           65          164          338          637 
TCGA-61-1725 TCGA-61-1728 TCGA-61-1733 TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 
         955          848          966         1484         1089           74 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1900 TCGA-61-1907 TCGA-61-1910 TCGA-61-1914 
        1024         1329          176          952         1126         1721 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
        1321          479         1161           60          168          441 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2088 TCGA-61-2092 
         931         1212          932           36          145         1573 
TCGA-61-2094 TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
        2182         1844         1992          197         2337          629 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
        1354         3824          676 
Variable 1:'AGE':	nDistinctValues=47,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=141,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=234,	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:'COMPLETENESS.OF.RESECTION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                         "KARNOFSKY.PERFORMANCE.SCORE"
[3] "TUMOR.STAGE"                
[1] "TUMOR.?STAGE" "3"           
[1] "stage2"
vv
  2   3   4 
 18 209  33 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 261 columns, 1 survival variables, and 3 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
KRTCAP3|200634 
          8663 
AGE, nv=47, binary=FALSE, numeric=TRUE
STS|412 
  15629 
KARNOFSKY.PERFORMANCE.SCORE, nv=3, binary=FALSE, numeric=TRUE
SNX2|6643 
    15224 
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "num to class table"
vv1
 60  80 100 
  5   8   1 
TUMOR.STAGE, nv=3, binary=FALSE, numeric=TRUE
BACE1|23621 
       1290 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 2 Stage 3 Stage 4 
     18     209      33 
> q(save="no")
