[1] "libdir: /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/ClinicalAnalysisAllGenes_new/broadinstitute.org/cancer.genome.analysis/00333/58/"
[1] "terrence_modification_tag: TRUE"
[1] "op: MUTATION_RATE"
[1] "dfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/OV-TP/5094652/OV-TP.patients.counts_and_rates.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/OV-TP/10006099/OV-TP.merged_data.txt"
[1] "gv: ALL"
[1] "gfn: "
[1] "sfn: "
[1] "fv: ALL"
[1] "ofn: "
[1] "dx: "
[1] "cfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/OV-TP/10006099/OV-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=586, in expression file=316, common to both=316
Number of genes in original expression dataset=2
[1] "ALL"
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                                      
 [2] "VITALSTATUS"                                       
 [3] "DAYSTODEATH"                                       
 [4] "DAYSTOLASTFOLLOWUP"                                
 [5] "PRIMARYSITEOFDESEASE"                              
 [6] "NEOPLASM.DISEASESTAGE"                             
 [7] "PATHOLOGY.T.STAGE"                                 
 [8] "PATHOLOGY.N.STAGE"                                 
 [9] "PATHOLOGY.M.STAGE"                                 
[10] "DCCUPLOADDATE"                                     
[11] "GENDER"                                            
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"                  
[13] "RADIATIONTHERAPY"                                  
[14] "KARNOFSKYPERFORMANCESCORE"                         
[15] "EXAMINATIONS.EXAMINATION.KARNOFSKYPERFORMANCESCORE"
[16] "HISTOLOGICALTYPE"                                  
[17] "TUMORGRADE"                                        
[18] "TUMORSTAGE"                                        
[19] "PATIENTTUMORRECURRENCESTATUS"                      
[20] "DAYSTOTUMORRECURRENCE"                             
[21] "CHEMOTHERAPY"                                      
[22] "RADIATIONS.RADIATION.REGIMENINDICATION"            
[23] "COMPLETENESS.OF.RESECTION"                         
[24] "RACE"                                              
[25] "ETHNICITY"                                         
[26] "BATCHNUMBER"                                       

Input Data has 26 rows and 316 columns.

[1] "Batch" "26"   
[1] "Last Follow UP"
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
        1224         1247         1495           NA         1418           NA 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
          NA         1993         1919           NA           NA           NA 
TCGA-04-1356 TCGA-04-1357 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
          NA           NA          989           NA           NA         2329 
TCGA-04-1367 TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 
        2174           NA           NA         1167           NA           NA 
TCGA-09-0366 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 
          NA           NA           NA           NA           NA           NA 
TCGA-09-1666 TCGA-09-1669 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 
        1752          928          186           NA         3419         2163 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
        1919         1209          379          788         2478          563 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 
        1011          982          356          119         1078          460 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 
         604          189          748         1355         1204           83 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 
         946          462          542         1678           76          351 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
        1036          981          869         1184         1117          873 
TCGA-13-0795 TCGA-13-0800 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
         596          247         1073          414         2097         3260 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
        2780         2259         2028         1881         2068         2099 
TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 
        1319         1509         1748         1708         1736         1441 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
        1470         1455         1367         1128          843         1036 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
         912          644          453          420          195          185 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
         331          201          224          184          180          208 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
         143          128          162         1662         2648         1877 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
         895         2982          681         2154         2521         1595 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
        2237         1162         1498          129         1652         1144 
TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
        1168          999          504          128          134          145 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2060 TCGA-20-0987 TCGA-20-0990 
         127           78           94          262           NA          789 
TCGA-20-0991 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
         797         1446         1294         1233          468          816 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 
         966         1503          886          575           68         1658 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 
         139         1013         2616          130         1189         1018 
TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
        1768          759         3525         2661         2788         2342 
TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
         232          598          354          663         1264          233 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
         679         1646         1933         1442          192          194 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
         238          243          239           23          190          183 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 
         181          163          147          529          583          568 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 
        1324          260         2218          379         1373          277 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 
         105           36          676          820         1746          493 
TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
        1721         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         2688         1470         1163 
TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 
         148         1769         1641          857         1354         1736 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
        1100           24           11         1446          962         2143 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 
        1357           25         2049         1102          506         1620 
TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 
         820         1553         1126           31         1064         1977 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1324 TCGA-25-1326 TCGA-25-1328 
        1124         1033           91         1035          945         1979 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
          90          565          548          481           11          627 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 
         239            9         1732         1843         1081         1558 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 
         396         1492           31         1157           92         1369 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
         608         1278           90          883          943          821 
TCGA-29-2427 TCGA-30-1853 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 
        1900         1103          186          914          571          204 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
          67          875          885          655          695          686 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-57-1582 
         260          915          783          847          737          731 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 
         346          643          763         5481           NA         3532 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1728 TCGA-61-1736 
          NA           NA           NA          165          848         1484 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 
        1161           61          168          441          547          122 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2088 TCGA-61-2092 
         932         1212          932           36          145         1573 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
        2182         1875         1844         1688          197         2338 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
         629         1354         3825          676 
Variable 1:'AGE':	nDistinctValues=50,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=172,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=271,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'EXAMINATIONS.EXAMINATION.KARNOFSKYPERFORMANCESCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'TUMOR.GRADE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'TUMOR.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 19:'PATIENTTUMORRECURRENCESTATUS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'DAYSTOTUMORRECURRENCE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 21:'CHEMOTHERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 23:'COMPLETENESS.OF.RESECTION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 24:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 25:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 26:'BATCH.NUMBER':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                         "KARNOFSKY.PERFORMANCE.SCORE"
[3] "RACE"                        "ETHNICITY"                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 316 columns, 1 survival variables, and 4 non-survival variables.
[1] "changed to 5 non-survival variables adding another age variable for linear regression analysis on mutaion rate."
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=50, binary=FALSE, numeric=TRUE
AGE_mutation.rate, nv=50, binary=FALSE, numeric=TRUE
$MUTATIONRATE_NONSYNONYMOUS

Call:
lm(formula = as.numeric(i) ~ vv)

Residuals:
       Min         1Q     Median         3Q        Max 
-1.531e-06 -6.974e-07 -2.441e-07  4.409e-07  3.853e-06 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)    
(Intercept) 1.365e-06  3.177e-07   4.298 2.32e-05 ***
vv          7.854e-09  5.190e-09   1.513    0.131    
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Residual standard error: 1.029e-06 on 306 degrees of freedom
  (8 observations deleted due to missingness)
Multiple R-squared: 0.007428,	Adjusted R-squared: 0.004184 
F-statistic:  2.29 on 1 and 306 DF,  p-value: 0.1313 


$MUTATIONRATE_SILENT

Call:
lm(formula = as.numeric(i) ~ vv)

Residuals:
       Min         1Q     Median         3Q        Max 
-5.691e-07 -1.978e-07 -5.226e-08  1.169e-07  9.409e-07 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)    
(Intercept) 3.324e-07  8.934e-08   3.721 0.000236 ***
vv          2.886e-09  1.460e-09   1.977 0.048926 *  
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Residual standard error: 2.895e-07 on 306 degrees of freedom
  (8 observations deleted due to missingness)
Multiple R-squared: 0.01261,	Adjusted R-squared: 0.009387 
F-statistic: 3.909 on 1 and 306 DF,  p-value: 0.04893 


KARNOFSKY.PERFORMANCE.SCORE, nv=4, binary=FALSE, numeric=TRUE
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "num to class table"
vv1
 40  60  80 100 
  2  13  36   5 
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
