[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/UCEC-TP/5093685/UCEC-TP.patients.counts_and_rates.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/UCEC-TP/10006384/UCEC-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/UCEC-TP/10006384/UCEC-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=497, in expression file=248, common to both=248
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] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 248 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
        1428         1126         2540           NA          997           98 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
        3205         2254         1750         2000         1841         1841 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
        1416         1167          860          633          706         2088 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VO 
         607          535          596          749          884          364 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AJ-A23M TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
        1288          485           36         2545           NA          181 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
          NA         2618          250         1199         1758         1385 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
        1122          239          636           NA         3815         3589 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
        3357          103         1921           NA         2972          965 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
        2554          825         2510           NA         1875         2457 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
        1497          763         1276           NA          603          903 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
        2079         2191         1413         1075         1399         2025 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
        1064         1640          833         1845         1065          868 
TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP 
        1149         1220         2004          516          412         1107 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        2167          589         2445         1731         1422         1312 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
        1237          990          871          862          928          788 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
         700          544          418          520          543          335 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
         265         5651         3448         2687         2303         1656 
TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
        1362         1337         1232          976         1019          832 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z 
         509          595          593          596          560          528 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
         504           NA           NA          566          614          588 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
         637         1071         1064          241         1167         1110 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
         860         1263         1477           NA         1309         1196 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
         937          644          617          469          742          811 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
         497         1043          868         1607         1721          451 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
         382          419          448          426          470          470 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
         721         1092         1064          189          311          309 
TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
         760           NA          714         2602         2379           NA 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
        2371         1882         2068         2935           NA         2963 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UM 
        2044         2687         2611         2506         2481         2644 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
        2212         2228         1910         1934         1507         2022 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
         512          602          911          260           17          148 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
         872          728          686           53          135          669 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
        1201          915          909           NA          112          892 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
         991           20          478         1098         1135         1106 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
        1141         1119           80           NA           NA          910 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
         945         1023          324           21          568          111 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
         532          594          917          548           48          213 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
          30          926           39          852          854          802 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
         311           46           54           NA          739           71 
TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A1LZ 
         697          402          555          496         1076         1471 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GS TCGA-EY-A212 TCGA-FI-A2D2 TCGA-FI-A2EW 
         332          328          459          110         1095         1795 
TCGA-FI-A2EX TCGA-FI-A2F8 
         276          761 
Variable 1:'AGE':	nDistinctValues=53,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=24,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=221,	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=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=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "HISTOLOGICAL.TYPE"                     
[3] "RADIATIONS.RADIATION.REGIMENINDICATION"
[4] "COMPLETENESS.OF.RESECTION"             
[5] "RACE"                                  
[6] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 248 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=53, binary=FALSE, numeric=TRUE
AGE_mutation.rate, nv=53, binary=FALSE, numeric=TRUE
$MUTATIONRATE_NONSYNONYMOUS

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

Residuals:
       Min         1Q     Median         3Q        Max 
-3.374e-05 -1.764e-05 -1.315e-05 -6.749e-06  2.897e-04 

Coefficients:
              Estimate Std. Error t value Pr(>|t|)   
(Intercept)  5.407e-05  1.940e-05   2.787  0.00573 **
vv          -5.763e-07  3.029e-07  -1.903  0.05826 . 
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Residual standard error: 5.28e-05 on 246 degrees of freedom
Multiple R-squared: 0.0145,	Adjusted R-squared: 0.0105 
F-statistic:  3.62 on 1 and 246 DF,  p-value: 0.05826 


$MUTATIONRATE_SILENT

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

Residuals:
       Min         1Q     Median         3Q        Max 
-9.188e-06 -5.246e-06 -3.804e-06 -1.933e-06  1.017e-04 

Coefficients:
              Estimate Std. Error t value Pr(>|t|)  
(Intercept)  1.441e-05  5.723e-06   2.518   0.0124 *
vv          -1.436e-07  8.934e-08  -1.607   0.1093  
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Residual standard error: 1.557e-05 on 246 degrees of freedom
Multiple R-squared: 0.01039,	Adjusted R-squared: 0.00637 
F-statistic: 2.584 on 1 and 246 DF,  p-value: 0.1093 


HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=5, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
