
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ClinicalAnalysisAllGenes_new.14.3949/ClinicalAnalysisAllGenes.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ClinicalAnalysisAllGenes_new.14.3949/", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/LAML-TB/3140714/0.GDAC_MethylationPreprocess.Finished/LAML-TB.meth.for_correlation.filtered_data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LAML-TB/3132663/1.GDAC_clinicalDataPicker.Finished/LAML-TB.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=197, in expression file=170, common to both=169
Number of genes in original expression dataset=16403
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                     "DAYSTODEATH"                     
 [3] "DAYSTOLASTFOLLOWUP"               "VITALSTATUS"                     
 [5] "DCCUPLOADDATE"                    "PRIMARYSITEOFDESEASE"            
 [7] "GENDER"                           "DATEOFINITIALPATHOLOGICDIAGNOSIS"
 [9] "DAYSTOLASTKNOWNALIVE"             "KARNOFSKYPERFORMANCESCORE"       
[11] "BATCHNUMBER"                     

Input Data has 11 rows and 169 columns.

[1] "Batch" "11"   
[1] "Last Follow UP"
TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 TCGA-AB-2810 TCGA-AB-2811 
          NA           NA           NA         2861           NA           NA 
TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 
          NA           NA           NA           NA           NA           NA 
TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2823 
          NA         2496           NA           NA           NA           NA 
TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2828 TCGA-AB-2830 TCGA-AB-2832 
          NA           NA           NA         2284           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-2851 
          NA           NA           NA           NA         2220           NA 
TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2856 TCGA-AB-2857 TCGA-AB-2858 
          NA           NA           NA           NA           NA           NA 
TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2866 TCGA-AB-2867 
          NA           NA         1430           NA           NA           NA 
TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 
          NA          243           NA          153          638          273 
TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2879 TCGA-AB-2880 TCGA-AB-2881 
         396          212          638          245          424          393 
TCGA-AB-2882 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2887 TCGA-AB-2888 
          NA           NA           NA          181           NA          334 
TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2891 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 
         304           NA           NA           NA           NA          243 
TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 
         393           NA           NA           58           NA           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-2924 TCGA-AB-2925 TCGA-AB-2927 TCGA-AB-2928 
          NA           NA           90           NA           NA           59 
TCGA-AB-2929 TCGA-AB-2930 TCGA-AB-2931 TCGA-AB-2932 TCGA-AB-2933 TCGA-AB-2934 
          NA           NA           NA           NA           NA           28 
TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2940 
          NA           59           NA           NA          455           NA 
TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2943 TCGA-AB-2944 TCGA-AB-2946 TCGA-AB-2948 
          NA          641           NA           NA           NA           NA 
TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 
         699          306           NA         1492           NA           NA 
TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 
          NA           NA         1277           NA           NA         1035 
TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2975 
        1127           NA           NA           NA           NA           NA 
TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2979 TCGA-AB-2980 TCGA-AB-2981 
          NA           NA          699          671          699          487 
TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 
         149           NA         1156           NA           NA           NA 
TCGA-AB-2988 TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2995 
          NA          457         1826           NA           NA         1551 
TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 
        1581           NA         1734         1249         1581           NA 
TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 
        2099           NA         1581           NA           NA         1885 
TCGA-AB-3012 
        1887 
Variable 1:'AGE':	nDistinctValues=61,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=61,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=50,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=9,	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:'BATCH.NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"    "GENDER"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 169 columns, 1 survival variables, and 2 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
AGRN 
 358 
AGE, nv=61, binary=FALSE, numeric=TRUE
JAKMIP1 
   7105 
GENDER, nv=2, binary=FALSE, numeric=FALSE
FAM35A 
  5026 
> q(save="no")
