
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/READ-TP/3527761/READ-TP.meth.by_min_expr_corr.data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/READ-TP/3352996/READ-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=333, in expression file=95, common to both=95
Number of genes in original expression dataset=20176
[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] "HISTOLOGICALTYPE"                      
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "DISTANT.METASTASIS"                    
[13] "LYMPH.NODE.METASTASIS"                 
[14] "COMPLETENESS.OF.RESECTION"             
[15] "NUMBER.OF.LYMPH.NODES"                 
[16] "TUMOR.STAGECODE"                       
[17] "NEOPLASM.DISEASESTAGE"                 
[18] "BATCHNUMBER"                           

Input Data has 18 rows and 95 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
         581          536          441          231          193          223 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3725 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
          NA           NA           NA           31           NA           30 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A026 
          NA           30         2130         1946          334           NA 
TCGA-AG-A02N TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
        1884         2192           15           44            6           21 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
          22          140           55          310          183          183 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
          NA          211          285          143          425         1825 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
         243          334          335          304          153          273 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
         224          212          849          212          608          180 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
         121          152            8         3635         1257         1741 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
        3683          734         1566          991           15           73 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
         232            5           66          250           14          121 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
          20          210          216          187          108          121 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
          83          159          237           84           62           NA 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
         103           26           66           12           31           20 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
          21           16           33           23           14           NA 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2690 
        1451           NA          636           NA           NA 
Variable 1:'AGE':	nDistinctValues=38,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=72,	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=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'TUMOR.STAGECODE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NEOPLASM.DISEASESTAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "GENDER"                                
 [3] "HISTOLOGICAL.TYPE"                     
 [4] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [5] "DISTANT.METASTASIS"                    
 [6] "LYMPH.NODE.METASTASIS"                 
 [7] "COMPLETENESS.OF.RESECTION"             
 [8] "NUMBER.OF.LYMPH.NODES"                 
 [9] "TUMOR.STAGECODE"                       
[10] "NEOPLASM.DISEASESTAGE"                 
[1] "TUMOR.?STAGE" "9"           
[1] "stage2"
vv
 T1  T2  T3  T4 T4A T4B 
  4  13  64   2   8   1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 95 columns, 1 survival variables, and 10 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
POU3F1 
 13719 
AGE, nv=38, binary=FALSE, numeric=TRUE
ATPAF2 
  1248 
GENDER, nv=2, binary=FALSE, numeric=FALSE
POLDIP3 
  13625 
HISTOLOGICAL.TYPE, nv=2, binary=FALSE, numeric=FALSE
LPAR5 
 9978 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
RSPO3 
15276 
DISTANT.METASTASIS, nv=4, binary=FALSE, numeric=FALSE
 TMC7 
17746 
LYMPH.NODE.METASTASIS, nv=9, binary=FALSE, numeric=FALSE
SH2D5 
15833 
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
CHID1 
 3729 
NUMBER.OF.LYMPH.NODES, nv=18, binary=FALSE, numeric=TRUE
JMJD7 
 8599 
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
[1] "Clinical variable TUMOR.STAGECODE has too few non-missing values, n=0"
NEOPLASM.DISEASESTAGE, nv=11, binary=FALSE, numeric=FALSE
ADRA2A 
   356 
> q(save="no")
