
R version 2.10.1 (2009-12-14)
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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/STAD-TP/3527770/STAD-TP.meth.by_min_expr_corr.data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/STAD-TP/3353011/STAD-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=375, in expression file=260, common to both=141
Number of genes in original expression dataset=19845
[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] "DISTANT.METASTASIS"                    
[12] "LYMPH.NODE.METASTASIS"                 
[13] "COMPLETENESS.OF.RESECTION"             
[14] "NUMBER.OF.LYMPH.NODES"                 
[15] "TUMOR.STAGECODE"                       
[16] "NEOPLASM.DISEASESTAGE"                 
[17] "BATCHNUMBER"                           

Input Data has 17 rows and 141 columns.

[1] "Batch" "17"   
[1] "Last Follow UP"
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6454 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
          29           NA           NA           43           NA           41 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
          41           26           25           19           19           52 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
          66           30           37           20           34           23 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
          20            8           37           45           14           38 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
           4           32           25           21            5          138 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 
          30           29           21            5           33           25 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
          40           21           29           15           14           22 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
           8           13            8           36           47           45 
TCGA-BR-8297 TCGA-BR-8483 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8682 TCGA-BR-8686 
          23           25            6           27           50           17 
TCGA-BR-8690 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
          18           18           28           12           24           NA 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
          24           16           13            4            7            3 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
          22           15           68           25           21           11 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CG-4437 
          15            9            2           NA           12          245 
TCGA-CG-4441 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
          NA           NA           NA           31           31           NA 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
         182           29         2131           NA           NA           NA 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
         944         1980          122         1674           NA           NA 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
         263          109          138          298          476          293 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
         249          210           21          181          201          126 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
          51          111           24          123           89          130 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
          19          237          199           61           NA           12 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
           6           92          109           31           NA           NA 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HF-7131 TCGA-HF-7132 
          86           17           30           47           NA           NA 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-7136 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
          NA           NA           NA           NA          209          108 
TCGA-IP-7968 TCGA-B7-5816 TCGA-B7-5818 
          77           NA           NA 
Variable 1:'AGE':	nDistinctValues=43,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=76,	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=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'HISTOLOGICAL.TYPE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DISTANT.METASTASIS':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'LYMPH.NODE.METASTASIS':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'COMPLETENESS.OF.RESECTION':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TUMOR.STAGECODE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NEOPLASM.DISEASESTAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'BATCH.NUMBER':	nDistinctValues=11,	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 T1A T1B  T2 T2A T2B  T3  T4 T4A T4B 
  1   1   2  25   2  11  62  16  16   3 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 141 columns, 1 survival variables, and 10 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
 PPT1 
13303 
AGE, nv=43, binary=FALSE, numeric=TRUE
PRTN3 
13529 
GENDER, nv=2, binary=FALSE, numeric=FALSE
KIF4B 
 8707 
HISTOLOGICAL.TYPE, nv=7, binary=FALSE, numeric=FALSE
 CAT 
2766 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
CBWD1 
 2794 
DISTANT.METASTASIS, nv=3, binary=FALSE, numeric=FALSE
UNC13B 
 18523 
LYMPH.NODE.METASTASIS, nv=5, binary=FALSE, numeric=FALSE
COX17 
 3923 
COMPLETENESS.OF.RESECTION, nv=3, binary=FALSE, numeric=FALSE
COPZ1 
 3896 
NUMBER.OF.LYMPH.NODES, nv=27, binary=FALSE, numeric=TRUE
RPS6KB2 
  14695 
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
ABCC4 
   62 
> q(save="no")
