
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.13.3873/ClinicalAnalysisAllGenes.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ClinicalAnalysisAllGenes_new.13.3873/", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/KIRP/1705789/0.GDAC_MethylationPreprocess.Finished/KIRP.meth.for_correlation.filtered_data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/KIRP/1669664/1.GDAC_clinicalDataPicker.Finished/KIRP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=95, in expression file=81, common to both=79
Number of genes in original expression dataset=20232
[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] "PATHOLOGICSPREAD(PT)"                  
[13] "PATHOLOGICSPREAD(PN)"                  
[14] "PATHOLOGICSPREAD(M)"                   
[15] "TUMORSTAGE"                            
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "NEOADJUVANTTHERAPY"                    
[18] "BATCHNUMBER"                           

Input Data has 18 rows and 79 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
           1           21          485            3           NA           NA 
TCGA-A4-7734 TCGA-A4-7828 TCGA-AL-7173 TCGA-B1-5398 TCGA-B9-5155 TCGA-B9-5156 
          27           NA         1357          336           19          196 
TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
          36         2638          585          269         1938          697 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
        1313         1454          658         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
         792          771          403          329          232           29 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
         364          240           84         3759           NA         2948 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
        2839           NA         1864         1532         1516          799 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
         612           NA          232          213          217          115 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
         353          414         3950         1093         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 
         418          114          445           92         2428         2459 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
        1556         1856         1669          471          178          160 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
         208          977         1257           NA          928         1059 
TCGA-G7-6797 TCGA-GL-6846 TCGA-GL-7773 TCGA-HE-7128 TCGA-HE-7129 TCGA-HE-7130 
         387         5558           NA           NA           NA           NA 
TCGA-J7-6720 
          NA 
Variable 1:'AGE':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=66,	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:'PATHOLOGY.T':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'PATHOLOGY.N':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'PATHOLOGICSPREAD(M)':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TUMOR.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'NEOADJUVANT.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                         "GENDER"                     
[3] "KARNOFSKY.PERFORMANCE.SCORE" "PATHOLOGY.T"                
[5] "PATHOLOGY.N"                 "PATHOLOGICSPREAD(M)"        
[7] "TUMOR.STAGE"                
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
 1  2  3  4 
44  3 21  8 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 79 columns, 1 survival variables, and 7 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
KCNF1 
 8380 
AGE, nv=34, binary=FALSE, numeric=TRUE
ZNF35 
19822 
GENDER, nv=2, binary=FALSE, numeric=FALSE
GLUD1 
 6796 
KARNOFSKY.PERFORMANCE.SCORE, nv=3, binary=FALSE, numeric=TRUE
GABRP 
 6504 
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "num to class table"
vv1
 40  90 100 
  1   9   9 
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
 PAX6 
13017 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
T1 T2 T3 T4 
47  3 28  1 
PATHOLOGY.N, nv=3, binary=FALSE, numeric=TRUE
HMX3 
7608 
[1] "PATHOLOGY.N"
[1] "num to class table"
vv1
N0 N1 N2 
19  8  4 
PATHOLOGICSPREAD(M), nv=3, binary=FALSE, numeric=FALSE
HSD3B2 
  7757 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
 PAX6 
13017 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
     44       3      21       8 
> q(save="no")
