[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/ACC-TP/8749121/ACC-TP.patients.counts_and_rates.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ACC-TP/10005775/ACC-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/ACC-TP/10005775/ACC-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=82, in expression file=91, common to both=81
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] "NEOPLASM.DISEASESTAGE"                 
 [6] "PATHOLOGY.T.STAGE"                     
 [7] "PATHOLOGY.N.STAGE"                     
 [8] "PATHOLOGY.M.STAGE"                     
 [9] "DCCUPLOADDATE"                         
[10] "GENDER"                                
[11] "RADIATIONTHERAPY"                      
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCHNUMBER"                           

Input Data has 15 rows and 81 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
          NA           NA         1942           NA           NA         2428 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC 
          NA           NA         1183           NA           NA           NA 
TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI 
        2782           NA         1259           NA         1227         1424 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
         309         1255          670           NA          889          149 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV 
         674         3688          383          488           NA         1541 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
        1924          950           NA          211         1029         2723 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 
          NA         2842          528          253         1130           NA 
TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
        1414         2673         4673         3659         1525         1091 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
          NA           NA         3897          724          840          628 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
         555          645          487           NA           NA           NA 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
          NA           NA         1589           NA           NA         2222 
TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
          NA         1916         1949         1583          639          882 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OF TCGA-P6-A5OG TCGA-P6-A5OH TCGA-PK-A5H8 
         365          709           NA           NA           NA         3240 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
         307          830         1293 
Variable 1:'AGE':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=29,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH.NUMBER':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
[4] "PATHOLOGY.N.STAGE"     "GENDER"                "ETHNICITY"            
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 81 columns, 1 survival variables, and 6 non-survival variables.
[1] "changed to 7 non-survival variables adding another age variable for linear regression analysis on mutaion rate."
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=46, binary=FALSE, numeric=TRUE
AGE_mutation.rate, nv=46, binary=FALSE, numeric=TRUE
$MUTATIONRATE_NONSYNONYMOUS

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

Residuals:
       Min         1Q     Median         3Q        Max 
-3.051e-06 -1.758e-06 -1.215e-06 -1.699e-07  2.762e-05 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)
(Intercept) 6.582e-07  1.469e-06   0.448    0.655
vv          4.085e-08  2.949e-08   1.385    0.170

Residual standard error: 4.227e-06 on 79 degrees of freedom
Multiple R-squared: 0.0237,	Adjusted R-squared: 0.01135 
F-statistic: 1.918 on 1 and 79 DF,  p-value: 0.17 


$MUTATIONRATE_SILENT

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

Residuals:
       Min         1Q     Median         3Q        Max 
-9.265e-07 -5.513e-07 -3.670e-07 -1.005e-07  1.022e-05 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)
(Intercept) 1.488e-07  5.041e-07   0.295    0.769
vv          1.435e-08  1.012e-08   1.418    0.160

Residual standard error: 1.451e-06 on 79 degrees of freedom
Multiple R-squared: 0.02481,	Adjusted R-squared: 0.01246 
F-statistic: 2.009 on 1 and 79 DF,  p-value: 0.1602 


NEOPLASM.DISEASESTAGE, nv=4, 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 
 8 38 11 19 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
