[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/STAD-TP/5093599/STAD-TP.patients.counts_and_rates.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/STAD-TP/10006301/STAD-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/STAD-TP/10006301/STAD-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=351, in expression file=221, common to both=221
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] "HISTOLOGICALTYPE"                      
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "COMPLETENESS.OF.RESECTION"             
[17] "NUMBER.OF.LYMPH.NODES"                 
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 221 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
         171          356           NA           NA           NA           NA 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-4292 TCGA-BR-4294 TCGA-BR-4357 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4361 TCGA-BR-4362 TCGA-BR-4363 TCGA-BR-4366 TCGA-BR-4368 TCGA-BR-4369 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4370 TCGA-BR-4371 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6454 TCGA-BR-6455 
          NA           NA         1055          485           NA          399 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
         308          416          213         1190           25           19 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
         997          421          402          491          273          642 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
         940          949         1002          390          280          753 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
         728          469          852           21            5          564 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 
         378           29           21           25           21           15 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 
         625           22           47           45          188          593 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
          90           29          418          131          101           11 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 
         583          450            8          482          113           22 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
         280          615          389          481           65          409 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8679 TCGA-BR-8680 TCGA-BR-8682 
         229           15          351           NA          481          500 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
          18           19          325          411          392           24 
TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4QI 
          NA           16           20          589          411          415 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
         352           86           99          400          401            9 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
           2           NA           12            2            2            2 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 
           3            4            5            3            3           NA 
TCGA-CD-8535 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
           4            3            3           NA           92          822 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
         485           NA          243          245         1645           NA 
TCGA-CG-4441 TCGA-CG-4442 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
          NA           NA          912         1431          580          366 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-4475 
          NA           NA          577           NA           NA          699 
TCGA-CG-4476 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
          NA          942           NA           31           31           NA 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
         183           30         3196           NA           NA         2405 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
        1980          122         1674           NA           NA          376 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
         385          363          582          625          573          564 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
         566          543          406          523          312          463 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
         486          389          321          344          375          752 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU 
         511          593          523          212          434          500 
TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
         180          449           19          200          440           NA 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
          12          594           92          678          519           NA 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7136 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
          NA           NA           NA           NA           NA          383 
TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GN TCGA-HU-A4GP 
         368           23          739          692          912          273 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
          NA          190          589          538          374          294 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
         645           NA          572           NA           77 
Variable 1:'AGE':	nDistinctValues=49,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=61,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=134,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'HISTOLOGICAL.TYPE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	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"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL.TYPE"                     
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "COMPLETENESS.OF.RESECTION"             
[10] "NUMBER.OF.LYMPH.NODES"                 
[11] "RACE"                                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 221 columns, 1 survival variables, and 11 non-survival variables.
[1] "changed to 12 non-survival variables adding another age variable for linear regression analysis on mutaion rate."
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=49, binary=FALSE, numeric=TRUE
AGE_mutation.rate, nv=49, binary=FALSE, numeric=TRUE
$MUTATIONRATE_NONSYNONYMOUS

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

Residuals:
       Min         1Q     Median         3Q        Max 
-1.528e-05 -9.077e-06 -6.593e-06 -1.467e-06  1.883e-04 

Coefficients:
              Estimate Std. Error t value Pr(>|t|)
(Intercept) -3.115e-06  9.468e-06  -0.329    0.742
vv           2.206e-07  1.408e-07   1.567    0.119

Residual standard error: 2.27e-05 on 214 degrees of freedom
  (5 observations deleted due to missingness)
Multiple R-squared: 0.01134,	Adjusted R-squared: 0.006723 
F-statistic: 2.455 on 1 and 214 DF,  p-value: 0.1186 


$MUTATIONRATE_SILENT

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

Residuals:
       Min         1Q     Median         3Q        Max 
-6.138e-06 -3.487e-06 -2.274e-06 -5.760e-07  6.835e-05 

Coefficients:
              Estimate Std. Error t value Pr(>|t|)  
(Intercept) -2.545e-06  3.330e-06  -0.764   0.4455  
vv           1.010e-07  4.952e-08   2.040   0.0426 *
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Residual standard error: 7.984e-06 on 214 degrees of freedom
  (5 observations deleted due to missingness)
Multiple R-squared: 0.01907,	Adjusted R-squared: 0.01449 
F-statistic: 4.161 on 1 and 214 DF,  p-value: 0.04259 


NEOPLASM.DISEASESTAGE, nv=11, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "PATHOLOGY.T.STAGE"
[1] "num to class table"
vv1
 1  2  3  4 
 7 66 90 49 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "PATHOLOGY.N.STAGE"
[1] "num to class table"
vv1
 0  1  2  3 
70 63 35 41 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=8, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=26, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
