
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/2008947/0.miRseq_preprocessor.Finished/STAD.miRseq_RPKM_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/STAD/1972820/1.GDAC_clinicalDataPicker.Finished/STAD.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=159, in expression file=151, common to both=150
Number of genes in original expression dataset=533
[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] "PATHOLOGICSPREAD(PT)"                  
[11] "PATHOLOGICSPREAD(PN)"                  
[12] "PATHOLOGICSPREAD(M)"                   
[13] "TUMORSTAGE"                            
[14] "RADIATIONS.RADIATION.REGIMENINDICATION"
[15] "NEOADJUVANTTHERAPY"                    
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 150 columns.

[1] "Batch" "16"   
[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-4190 TCGA-BR-4191 TCGA-BR-4194 TCGA-BR-4195 TCGA-BR-4199 TCGA-BR-4200 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4259 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4261 TCGA-BR-4265 TCGA-BR-4267 TCGA-BR-4277 TCGA-BR-4278 TCGA-BR-4279 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4280 TCGA-BR-4281 TCGA-BR-4284 TCGA-BR-4291 TCGA-BR-4292 TCGA-BR-4294 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4298 TCGA-BR-4357 TCGA-BR-4361 TCGA-BR-4362 TCGA-BR-4363 TCGA-BR-4366 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4367 TCGA-BR-4368 TCGA-BR-4369 TCGA-BR-4370 TCGA-BR-4371 TCGA-BR-4375 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4376 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6454 TCGA-BR-6455 TCGA-BR-6456 
          NA           29           NA           NA           43           NA 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
          41           41           26           25           19           19 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
          52           66           30           37           20           34 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 
          23           20            8           37           14           38 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-CD-5798 
           4           32           25           21          138           25 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
          21           11           15            9            2           NA 
TCGA-CD-5813 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
          12          609           92          822          485           31 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4442 
        1611          245         1644          122          426           NA 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
         912         1431          366          669           31          273 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4475 TCGA-CG-4476 
         576          215          365           31           NA           NA 
TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
          31           31          211           31           31           30 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
         182           29         2131          366          457          881 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
         944         1980          122         1674          641          243 
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          143          123           89          130 
TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
          19          199           61           NA           12            6 
TCGA-HF-7131 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-7136 TCGA-IN-7806 
          NA           NA           NA           NA           NA          209 
Variable 1:'AGE':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=15,	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=4,	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=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'PATHOLOGY.T':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'PATHOLOGY.N':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'PATHOLOGICSPREAD(M)':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'TUMOR.STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "HISTOLOGICAL.TYPE"                     
[4] "PATHOLOGY.T"                           
[5] "PATHOLOGY.N"                           
[6] "PATHOLOGICSPREAD(M)"                   
[7] "TUMOR.STAGE"                           
[8] "RADIATIONS.RADIATION.REGIMENINDICATION"
[9] "NEOADJUVANT.THERAPY"                   
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
 1  2  3  4 
24 35 38 25 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 150 columns, 1 survival variables, and 9 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
HSA-MIR-607 
        465 
AGE, nv=45, binary=FALSE, numeric=TRUE
HSA-MIR-183 
        130 
GENDER, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-3611 
         291 
HISTOLOGICAL.TYPE, nv=6, binary=FALSE, numeric=FALSE
HSA-MIR-33A 
        277 
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
HSA-MIR-200B 
         161 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
T1 T2 T3 T4 
 6 51 55 17 
PATHOLOGY.N, nv=4, binary=FALSE, numeric=TRUE
HSA-MIR-3926-2 
           351 
[1] "PATHOLOGY.N"
[1] "num to class table"
vv1
N0 N1 N2 N3 
43 54 22 13 
PATHOLOGICSPREAD(M), nv=3, binary=FALSE, numeric=FALSE
HSA-MIR-1255A 
           46 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
HSA-MIR-200B 
         161 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
     24      35      38      25 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-3150 
         235 
NEOADJUVANT.THERAPY, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-514-1 
          411 
> q(save="no")
