
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/BLCA/1780748/0.miRseq_preprocessor.Finished/BLCA.miRseq_RPKM_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/BLCA/1708518/1.GDAC_clinicalDataPicker.Finished/BLCA.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=69, in expression file=88, common to both=67
Number of genes in original expression dataset=591
[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] "KARNOFSKYPERFORMANCESCORE"             
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "NEOADJUVANTTHERAPY"                    
[13] "BATCHNUMBER"                           

Input Data has 13 rows and 67 columns.

[1] "Batch" "13"   
[1] "Last Follow UP"
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
         389           NA           NA           NA           NA          363 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
          NA           NA           NA           NA           NA           NA 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-C4-A0EZ 
          NA           NA           NA           NA           NA           NA 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS 
          59           88           61           NA           14           13 
TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1A3 TCGA-DK-A1A5 
          21           NA           NA          219           77           NA 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
         955          273          214          271         3616         3056 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
         218          178          202           55          322           NA 
TCGA-DK-A2I6 TCGA-DK-A3IS TCGA-E5-A2PC TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
        2291         1151         1108          268          253           NA 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF 
         209           NA          336           71          417         1497 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
         806          172           NA          684          525          214 
TCGA-G2-A3IE TCGA-GC-A3I6 TCGA-GD-A2C5 TCGA-GV-A3JW TCGA-GV-A3JX TCGA-H4-A2HO 
          NA           68          234          160          187           46 
TCGA-H4-A2HQ 
         204 
Variable 1:'AGE':	nDistinctValues=35,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=24,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=41,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=3,	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:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'BATCH.NUMBER':	nDistinctValues=17,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                         "GENDER"                     
[3] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 67 columns, 1 survival variables, and 3 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
HSA-MIR-3193 
         268 
AGE, nv=35, binary=FALSE, numeric=TRUE
HSA-MIR-23B 
        204 
GENDER, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-1-1 
         12 
KARNOFSKY.PERFORMANCE.SCORE, nv=5, binary=FALSE, numeric=TRUE
HSA-MIR-485 
        406 
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "num to class table"
vv1
40 60 70 80 90 
 2  1  1  2 10 
> q(save="no")
