[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/PCPG-TP/10011100/PCPG-TP.patients.counts_and_rates.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PCPG-TP/10006138/PCPG-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/PCPG-TP/10006138/PCPG-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=61, in expression file=178, common to both=61
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] "DCCUPLOADDATE"                         
 [6] "GENDER"                                
 [7] "RADIATIONTHERAPY"                      
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "RACE"                                  
[10] "ETHNICITY"                             
[11] "BATCHNUMBER"                           

Input Data has 11 rows and 61 columns.

[1] "Batch" "11"   
[1] "Last Follow UP"
TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
         883           69           29          179          240         1094 
TCGA-PR-A5PH TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
         852          773          211           55           22          766 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RT-A6Y9 TCGA-RT-A6YA 
          70          134           24           29         2957         1249 
TCGA-RT-A6YC TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 
         246          604           89          216         1013          724 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D 
          32           26           37          356          191         2214 
TCGA-RW-A7D0 TCGA-SP-A6QD TCGA-SP-A6QH TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
          54         3087         1857         2983          274         3013 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MR TCGA-SR-A6MS TCGA-SR-A6MT 
          43            3         1558         2020         2222         3247 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
        3362         3269           NA          456          345         1106 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7HA 
         132          765          242          317          770           36 
TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A815 
         218          195          137          188           24          182 
TCGA-XG-A823 
         210 
Variable 1:'AGE':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=TRUE.
Variable 3:'DAYSTODEATH':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'BATCH.NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"    "GENDER" "RACE"  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 61 columns, 0 survival variables, and 3 non-survival variables.
[1] "changed to 4 non-survival variables adding another age variable for linear regression analysis on mutaion rate."
AGE, nv=39, binary=FALSE, numeric=TRUE
AGE_mutation.rate, nv=39, binary=FALSE, numeric=TRUE
$MUTATIONRATE_NONSYNONYMOUS

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

Residuals:
       Min         1Q     Median         3Q        Max 
-2.930e-07 -1.140e-07 -4.171e-08  6.716e-08  4.495e-07 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)   
(Intercept) 2.315e-07  8.025e-08   2.885  0.00547 **
vv          3.503e-09  1.568e-09   2.233  0.02934 * 
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Residual standard error: 1.672e-07 on 59 degrees of freedom
Multiple R-squared: 0.07794,	Adjusted R-squared: 0.06232 
F-statistic: 4.987 on 1 and 59 DF,  p-value: 0.02934 


$MUTATIONRATE_SILENT

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

Residuals:
       Min         1Q     Median         3Q        Max 
-1.522e-07 -6.335e-08 -9.220e-09  5.264e-08  2.793e-07 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)  
(Intercept) 8.343e-08  4.142e-08   2.014   0.0485 *
vv          1.075e-09  8.095e-10   1.328   0.1894  
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Residual standard error: 8.629e-08 on 59 degrees of freedom
Multiple R-squared: 0.02901,	Adjusted R-squared: 0.01255 
F-statistic: 1.763 on 1 and 59 DF,  p-value: 0.1894 


GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
