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

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/CESC-TP/2900410/0.GDAC_MethylationPreprocess.Finished/CESC-TP.meth.for_correlation.filtered_data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/CESC-TP/2843106/1.GDAC_clinicalDataPicker.Finished/CESC-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=37, in expression file=116, common to both=33
Number of genes in original expression dataset=17326
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "HISTOLOGICALTYPE"                      
[10] "RADIATIONS.RADIATION.REGIMENINDICATION"
[11] "NUMBERPACKYEARSSMOKED"                 
[12] "TOBACCOSMOKINGHISTORYINDICATOR"        
[13] "DISTANT.METASTASIS"                    
[14] "LYMPH.NODE.METASTASIS"                 
[15] "NUMBER.OF.LYMPH.NODES"                 
[16] "TUMOR.STAGECODE"                       
[17] "BATCHNUMBER"                           

Input Data has 17 rows and 33 columns.

[1] "Batch" "17"   
[1] "Last Follow UP"
TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN 
          NA           NA         1616           NA           NA           NA 
TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
        2382         2155         1289           NA           81         2127 
TCGA-DS-A0VN TCGA-DS-A1OB TCGA-DS-A1OC TCGA-DS-A1OD TCGA-DS-A3LQ TCGA-EA-A1QT 
        2892           NA          376         3096          183            8 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EK-A2PI 
          53           40           25           19           81           NA 
TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
         178           37           37           30           66            2 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA 
          31           44          773 
Variable 1:'AGE':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=24,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'NUMBERPACKYEARSSMOKED':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'DISTANT.METASTASIS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'LYMPH.NODE.METASTASIS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'TUMOR.STAGECODE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'BATCH.NUMBER':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "HISTOLOGICAL.TYPE"                     
[3] "RADIATIONS.RADIATION.REGIMENINDICATION"
[4] "NUMBERPACKYEARSSMOKED"                 
[5] "TOBACCOSMOKINGHISTORYINDICATOR"        
[6] "DISTANT.METASTASIS"                    
[7] "LYMPH.NODE.METASTASIS"                 
[8] "NUMBER.OF.LYMPH.NODES"                 
[9] "TUMOR.STAGECODE"                       
[1] "TUMOR.?STAGE" "9"           
[1] "stage2"
vv
 T1B T1B1 T1B2  T2A T2A1 T2A2  T2B  T3B 
   4   11    5    2    1    2    3    1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 33 columns, 1 survival variables, and 9 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
TCP10L 
 14919 
AGE, nv=25, binary=FALSE, numeric=TRUE
IGFBP7 
  7254 
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
LOC100302640 
        8490 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
PRMT1 
11900 
NUMBERPACKYEARSSMOKED, nv=8, binary=FALSE, numeric=TRUE
 PNKP 
11564 
TOBACCOSMOKINGHISTORYINDICATOR, nv=4, binary=FALSE, numeric=TRUE
CHMP4B 
  3284 
[1] "TOBACCOSMOKINGHISTORYINDICATOR"
[1] "num to class table"
vv1
 1  2  3  4 
15  9  1  5 
DISTANT.METASTASIS, nv=2, binary=FALSE, numeric=FALSE
CTSC 
3912 
LYMPH.NODE.METASTASIS, nv=2, binary=FALSE, numeric=FALSE
PRPF40A 
  11934 
NUMBER.OF.LYMPH.NODES, nv=5, binary=FALSE, numeric=TRUE
NDUFS5 
 10162 
[1] "NUMBER.OF.LYMPH.NODES"
[1] "num to class table"
vv1
 0  1  2  4 16 
19  6  2  1  1 
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
[1] "Clinical variable TUMOR.STAGECODE has too few non-missing values, n=0"
> q(save="no")
