
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/KIRP-TP/3527724/KIRP-TP.meth.by_min_expr_corr.data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/KIRP-TP/3351306/KIRP-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=101, in expression file=111, common to both=85
Number of genes in original expression dataset=20125
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "KARNOFSKYPERFORMANCESCORE"             
[11] "HISTOLOGICALTYPE"                      
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "NUMBERPACKYEARSSMOKED"                 
[14] "YEAROFTOBACCOSMOKINGONSET"             
[15] "DISTANT.METASTASIS"                    
[16] "LYMPH.NODE.METASTASIS"                 
[17] "TUMOR.STAGECODE"                       
[18] "NEOPLASM.DISEASESTAGE"                 
[19] "BATCHNUMBER"                           

Input Data has 19 rows and 85 columns.

[1] "Batch" "19"   
[1] "Last Follow UP"
TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 
           3           NA           NA            1           27           NA 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 
           7           49          140         1357          336          223 
TCGA-B3-8121 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 
         147           19          196           36         2638          585 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
         269         1938          697         1313         1454          658 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
        1242          792          921          792          771          403 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
         329          232           29          364          240           84 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
        3759           NA         2948         2839           NA         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
        1532         1516          799          612           NA          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         213          217          115          353          414         3950 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
        1093         1142          744          418          114          445 
TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
          92         2428         2459         1556         1856         1669 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
         471          178          160          208          977         1257 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
          NA          928         1059          387          445          428 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-HE-7128 TCGA-HE-7129 TCGA-HE-7130 
        5558           NA          112           NA           NA           NA 
TCGA-J7-6720 
          NA 
Variable 1:'AGE':	nDistinctValues=37,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=71,	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=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=24,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'NUMBERPACKYEARSSMOKED':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'DISTANT.METASTASIS':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'LYMPH.NODE.METASTASIS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'TUMOR.STAGECODE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'BATCH.NUMBER':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                         "GENDER"                     
[3] "KARNOFSKY.PERFORMANCE.SCORE" "DISTANT.METASTASIS"         
[5] "LYMPH.NODE.METASTASIS"       "TUMOR.STAGECODE"            
[7] "NEOPLASM.DISEASESTAGE"      
[1] "TUMOR.?STAGE" "6"           
[1] "stage2"
vv
 T1 T1A T1B  T2 T2A T2B  T3 T3A T3B  T4 
  7  30  12   3   2   1   6  16   7   1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 85 columns, 1 survival variables, and 7 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
 SYT2 
17167 
AGE, nv=37, binary=FALSE, numeric=TRUE
ACOT8 
  177 
GENDER, nv=2, binary=FALSE, numeric=FALSE
ATAD5 
 1135 
KARNOFSKY.PERFORMANCE.SCORE, nv=3, binary=FALSE, numeric=TRUE
LRRC14B 
  10056 
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "num to class table"
vv1
 40  90 100 
  1  10   9 
DISTANT.METASTASIS, nv=3, binary=FALSE, numeric=FALSE
ERCC2 
 5681 
LYMPH.NODE.METASTASIS, nv=4, binary=FALSE, numeric=FALSE
TMEM132B 
   17733 
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
[1] "Clinical variable TUMOR.STAGECODE has too few non-missing values, n=0"
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
DLX6AS__1 
     4987 
> q(save="no")
