[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/LAML-TB/6159038/LAML-TB.patients.counts_and_rates.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LAML-TB/10005979/LAML-TB.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/LAML-TB/10005979/LAML-TB.merged_data.txt"
[1] "ok3"

nSamples in clinical file=200, in expression file=197, common to both=197
Number of genes in original expression dataset=2
[1] "ALL"
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                     "VITALSTATUS"                     
 [3] "DAYSTODEATH"                      "DAYSTOLASTFOLLOWUP"              
 [5] "PRIMARYSITEOFDESEASE"             "DCCUPLOADDATE"                   
 [7] "GENDER"                           "DATEOFINITIALPATHOLOGICDIAGNOSIS"
 [9] "DAYSTOLASTKNOWNALIVE"             "KARNOFSKYPERFORMANCESCORE"       
[11] "RACE"                             "ETHNICITY"                       
[13] "BATCHNUMBER"                     

Input Data has 13 rows and 197 columns.

[1] "Batch" "13"   
[1] "Last Follow UP"
TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 
          NA           NA         2557           NA           NA           NA 
TCGA-AB-2808 TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 
        2861           NA           NA           NA           NA           NA 
TCGA-AB-2814 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 
          NA           NA           NA           NA         2496           NA 
TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 
          NA           NA           NA           NA           NA           NA 
TCGA-AB-2827 TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 
          NA         2284           NA           NA           NA           NA 
TCGA-AB-2833 TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 
          NA           NA         1673           NA           NA           NA 
TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2843 TCGA-AB-2844 
          NA           NA           NA           NA           NA           NA 
TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2847 TCGA-AB-2848 TCGA-AB-2849 TCGA-AB-2850 
          NA           NA           NA           NA         2220           NA 
TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2857 TCGA-AB-2858 
          NA           NA           NA           NA           NA           NA 
TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 
          NA           NA           NA         1430           NA           NA 
TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 
          NA           NA           NA           NA          243           NA 
TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2876 
         153          638          273          396          212         1219 
TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2880 TCGA-AB-2881 TCGA-AB-2882 
         638           NA          245          424          393           NA 
TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2887 TCGA-AB-2888 
         730           NA           NA          181           NA          334 
TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2891 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 
         304           NA           NA          943           NA           NA 
TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 
          NA           NA          243          393           NA           NA 
TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2907 
          59           NA           NA         1611          577           NA 
TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 
          NA           30           NA         1186           NA         1216 
TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2918 TCGA-AB-2919 
         792           NA          882         1216           NA           61 
TCGA-AB-2920 TCGA-AB-2921 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 
          NA           NA           NA           NA           90           NA 
TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2928 TCGA-AB-2929 TCGA-AB-2930 TCGA-AB-2931 
          NA           NA           59           NA           NA           NA 
TCGA-AB-2932 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 
          NA           NA           28           NA           59           NA 
TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2940 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2943 
          NA          455           NA           NA          641           NA 
TCGA-AB-2945 TCGA-AB-2946 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 
          NA           NA           31           NA          699          306 
TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 
          NA         1492           NA           NA          609           NA 
TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 
          NA         1277           NA           NA         1035           NA 
TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 
        1127           NA           NA           NA           NA           NA 
TCGA-AB-2975 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2979 TCGA-AB-2980 
          NA           NA           NA          699          671          699 
TCGA-AB-2981 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 
         487          150           NA         1157           NA           NA 
TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 
          NA           NA           NA          457         1826           NA 
TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2997 TCGA-AB-2998 
          NA         1798         1551         1581           NA           NA 
TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 
        1735         1249         1581           NA         2100           NA 
TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
        1581           NA           NA         1885         1887 
Variable 1:'AGE':	nDistinctValues=62,	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=58,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'BATCH.NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"       "GENDER"    "RACE"      "ETHNICITY"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 197 columns, 1 survival variables, and 4 non-survival variables.
[1] "changed to 5 non-survival variables adding another age variable for linear regression analysis on mutaion rate."
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=62, binary=FALSE, numeric=TRUE
AGE_mutation.rate, nv=62, binary=FALSE, numeric=TRUE
$MUTATIONRATE_NONSYNONYMOUS

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

Residuals:
       Min         1Q     Median         3Q        Max 
-3.390e-07 -1.450e-07  1.570e-09  1.122e-07  9.369e-07 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)    
(Intercept) 1.472e-07  4.659e-08   3.158 0.001839 ** 
vv          2.864e-09  8.122e-10   3.526 0.000526 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Residual standard error: 1.839e-07 on 195 degrees of freedom
Multiple R-squared: 0.05993,	Adjusted R-squared: 0.05511 
F-statistic: 12.43 on 1 and 195 DF,  p-value: 0.0005263 


$MUTATIONRATE_SILENT

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

Residuals:
       Min         1Q     Median         3Q        Max 
-1.017e-07 -4.974e-08 -1.457e-08  3.586e-08  2.278e-07 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)  
(Intercept) 3.990e-08  1.755e-08   2.273   0.0241 *
vv          7.630e-10  3.060e-10   2.494   0.0135 *
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Residual standard error: 6.927e-08 on 195 degrees of freedom
Multiple R-squared: 0.03091,	Adjusted R-squared: 0.02594 
F-statistic: 6.219 on 1 and 195 DF,  p-value: 0.01347 


GENDER, 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 "
