
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/miRseq_preprocessor/STAD-TP/3472001/0.miRseq_preprocessor.Finished/STAD-TP.miRseq_RPKM_log2.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=378, in expression file=286, common to both=184
Number of genes in original expression dataset=510
[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 184 columns.

[1] "Batch" "17"   
[1] "Last Follow UP"
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
         171            3           NA           NA           NA           NA 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-4292 TCGA-BR-4294 TCGA-BR-4357 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4361 TCGA-BR-4362 TCGA-BR-4363 TCGA-BR-4366 TCGA-BR-4367 TCGA-BR-4368 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4369 TCGA-BR-4370 TCGA-BR-4371 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6454 
          NA           NA           NA           29           NA           NA 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
          43           NA           41           41           26           25 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
          19           19           52           66           30           37 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
          20           34           23           20            8           37 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
          45           14           38            4           32           25 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
          21            5          138           30           29           21 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
           5           33           25           40           21           29 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
          15           14           22            8           13            8 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8483 TCGA-BR-8592 
          36           47           45           23           25            6 
TCGA-BR-8676 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A4IU TCGA-BR-A4IV 
          27           50           17           18           18           28 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
          12           24           NA            4            7            3 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
          68           25           21           11           15            9 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
           2           NA           12           NA           92          822 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
         485           NA          242          245         1644           NA 
TCGA-CG-4441 TCGA-CG-4442 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
          NA           NA          912         1431          580          366 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
          NA           NA           NA          576           NA          365 
TCGA-CG-4474 TCGA-CG-4475 TCGA-CG-4476 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
          NA           NA           NA           31           NA           NA 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
          31           31           NA          182           29         2131 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
          NA           NA           NA          944         1980          122 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        1674           NA           NA          263          109          138 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
         298          476          293          249          210           21 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
         181          201          126           51          111           24 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 
         123           89          130           19          237          199 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
          61           NA           12            6           92          109 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
          31           NA           NA           86           17           30 
TCGA-FP-A4BF TCGA-HF-7131 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-7136 
          47           NA           NA           NA           NA           NA 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
          NA          209          108           77 
Variable 1:'AGE':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=86,	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=11,	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=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=30,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TUMOR.STAGECODE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NEOPLASM.DISEASESTAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'BATCH.NUMBER':	nDistinctValues=15,	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  TX 
  3   1   2  30  10  14  73  23  14   4  10 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 184 columns, 1 survival variables, and 10 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
HSA-MIR-296 
        200 
AGE, nv=48, binary=FALSE, numeric=TRUE
HSA-MIR-183 
        126 
GENDER, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-495 
        374 
HISTOLOGICAL.TYPE, nv=7, binary=FALSE, numeric=FALSE
HSA-MIR-577 
        430 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-548F-1 
           409 
DISTANT.METASTASIS, nv=3, binary=FALSE, numeric=FALSE
HSA-MIR-138-2 
           90 
LYMPH.NODE.METASTASIS, nv=6, binary=FALSE, numeric=FALSE
HSA-LET-7F-2 
           9 
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
HSA-LET-7F-2 
           9 
NUMBER.OF.LYMPH.NODES, nv=30, binary=FALSE, numeric=TRUE
HSA-MIR-653 
        459 
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
HSA-MIR-217 
        175 
> q(save="no")
