[1] "libdir: /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/ClinicalAnalysisAllGenes_new/broadinstitute.org/cancer.genome.analysis/00333/60/"
[1] "terrence_modification_tag: TRUE"
[1] "op: MUTATION_RATE"
[1] "dfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/GBM-TP/5094119/GBM-TP.patients.counts_and_rates.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/GBM-TP/11541538/GBM-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/GBM-TP/11541538/GBM-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=587, in expression file=283, common to both=278
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] "PRIMARYSITEOFDISEASE"                  
 [6] "DCCUPLOADDATE"                         
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "RADIATIONTHERAPY"                      
[10] "KARNOFSKYPERFORMANCESCORE"             
[11] "HISTOLOGICALTYPE"                      
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCHNUMBER"                           

Input Data has 15 rows and 278 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
TCGA-02-0003 TCGA-02-0033 TCGA-02-0047 TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 
         144           86          448           76          393          466 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 
         470          493           NA            8          123            3 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 
         691          989          320          570          702          327 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 TCGA-06-0151 TCGA-06-0152 
          NA          280           NA           71           NA          359 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 
         389          263           97          166           NA          161 
TCGA-06-0167 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 
          NA          579           95            7           67         1642 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 
        1228         2246          866          454          557          214 
TCGA-06-0209 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 
         119            6          378          684           11          315 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
         359           NA          455          375           98          136 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
         294           62          717          286          679          595 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
         164           82           66           28         1322         1405 
TCGA-06-0877 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
         204          218          699          178          165          637 
TCGA-06-1804 TCGA-06-1806 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
         414           NA           33           23          150          282 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 
          86          932          181          207          133           13 
TCGA-06-2570 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
         958          342          108          254          138          268 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
         273          260          155           83          114          187 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6389 TCGA-06-6390 TCGA-06-6391 TCGA-06-6693 
         139          120          237          164           45           15 
TCGA-06-6694 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
         224          253          391          145           47          145 
TCGA-06-6701 TCGA-08-0386 TCGA-12-0615 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
         151          478          426          439           50          316 
TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 
         734           80          323          427          351          333 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 
        1050          357          399           98           62          364 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0787 TCGA-14-0789 TCGA-14-0790 TCGA-14-0813 
          29          701           68          342          419           41 
TCGA-14-0817 TCGA-14-0862 TCGA-14-0871 TCGA-14-1043 TCGA-14-1395 TCGA-14-1450 
         164           88          880           24           42         1788 
TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 
        1246          543          232          218          532           12 
TCGA-14-4157 TCGA-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-16-0861 TCGA-16-1045 
         104          300           NA          119          131          883 
TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 TCGA-19-2623 TCGA-19-2624 
         772          154          294          148          229            5 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 TCGA-19-5947 TCGA-19-5950 
         124          501          213          137          202          343 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 
         244          567          144          242           54          164 
TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 TCGA-26-1442 TCGA-26-5132 TCGA-26-5133 
         161          165          422          953          286          452 
TCGA-26-5134 TCGA-26-5135 TCGA-26-5136 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
         167          270           37           48          241           71 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
         146          505           NA          555         1008          648 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
         914          427          350          753          316          316 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 
         489          231           87          438          480           77 
TCGA-28-1753 TCGA-28-2499 TCGA-28-2502 TCGA-28-2509 TCGA-28-2513 TCGA-28-2514 
          37           95           20          145          222          160 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
         119          275          474          442          358          951 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
         432          237          415          128          690          319 
TCGA-28-6450 TCGA-32-1970 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
         165          468            3          593           36          142 
TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
         386          515          372          632          457          485 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 TCGA-32-4210 
         269          693          644          643          604          113 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
         383          604          330          323           26          406 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 
         272          290           30          135          360            6 
TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
         351          236          105          636          132          436 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 
         228          146          138          535           94          111 
TCGA-76-4931 TCGA-76-4932 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
         279         1458           77          328          508          100 
TCGA-76-6193 TCGA-76-6280 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
          82          346          519          254          638          147 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-81-5910 
         153            7          282          235          237           49 
TCGA-81-5911 TCGA-87-5896 
         539          800 
Variable 1:'AGE':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=187,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=230,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'DCCUPLOADDAY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH.NUMBER':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "KARNOFSKY.PERFORMANCE.SCORE"           
[4] "HISTOLOGICAL.TYPE"                     
[5] "RADIATIONS.RADIATION.REGIMENINDICATION"
[6] "RACE"                                  
[7] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 278 columns, 1 survival variables, and 7 non-survival variables.
[1] "changed to 8 non-survival variables adding another age variable for linear regression analysis on mutaion rate."
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=59, binary=FALSE, numeric=TRUE
AGE_mutation.rate, nv=59, binary=FALSE, numeric=TRUE
$MUTATIONRATE_NONSYNONYMOUS

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

Residuals:
       Min         1Q     Median         3Q        Max 
-1.467e-06 -3.601e-07 -6.060e-08  2.808e-07  3.678e-06 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)    
(Intercept) 7.737e-07  1.729e-07   4.474 1.12e-05 ***
vv          1.432e-08  2.771e-09   5.169 4.52e-07 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Residual standard error: 5.996e-07 on 276 degrees of freedom
Multiple R-squared: 0.08826,	Adjusted R-squared: 0.08496 
F-statistic: 26.72 on 1 and 276 DF,  p-value: 4.522e-07 


$MUTATIONRATE_SILENT

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

Residuals:
       Min         1Q     Median         3Q        Max 
-5.070e-07 -1.427e-07 -2.308e-08  1.178e-07  2.020e-06 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)    
(Intercept) 1.661e-07  7.171e-08   2.316   0.0213 *  
vv          6.196e-09  1.149e-09   5.393 1.49e-07 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Residual standard error: 2.486e-07 on 276 degrees of freedom
Multiple R-squared: 0.09532,	Adjusted R-squared: 0.09204 
F-statistic: 29.08 on 1 and 276 DF,  p-value: 1.492e-07 


GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
