
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-TP/2281982/0.miRseq_preprocessor.Finished/BLCA-TP.miRseq_RPKM_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/BLCA-TP/2170312/1.GDAC_clinicalDataPicker.Finished/BLCA-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=108, in expression file=124, common to both=103
Number of genes in original expression dataset=582
[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] "RADIATIONTHERAPY"                      
[11] "KARNOFSKYPERFORMANCESCORE"             
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "NUMBERPACKYEARSSMOKED"                 
[14] "STOPPEDSMOKINGYEAR"                    
[15] "TOBACCOSMOKINGHISTORYINDICATOR"        
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 103 columns.

[1] "Batch" "16"   
[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-BT-A2LA 
          NA           NA           NA           NA           NA          179 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
         111           NA           NA           59           88           61 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
          NA           14           13           21           NA           NA 
TCGA-CF-A3MH TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL 
          NA           NA           NA          219          166          246 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
          77           NA          955          273          214          271 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
        3616         3056          218          178          202           55 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
         322           NA         2291           67          121          238 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-E5-A2PC TCGA-FD-A3B3 
         319         1151          168           NA         1108          268 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
         253           NA          209           NA          336          272 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
         242          974          334          207           NA          138 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF 
          NA           NA           59           71          417         1884 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
         806          172           NA          997          525          214 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3I6 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
          NA           25           68          234           64           95 
TCGA-GD-A3OS TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QG 
         177          133          160          187          232           NA 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS 
         237          125           46          204           NA          265 
TCGA-K4-A3WV 
         141 
Variable 1:'AGE':	nDistinctValues=43,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=29,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=67,	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=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'NUMBERPACKYEARSSMOKED':	nDistinctValues=30,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'STOPPEDSMOKINGYEAR':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                            "GENDER"                        
[3] "KARNOFSKY.PERFORMANCE.SCORE"    "NUMBERPACKYEARSSMOKED"         
[5] "STOPPEDSMOKINGYEAR"             "TOBACCOSMOKINGHISTORYINDICATOR"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 103 columns, 1 survival variables, and 6 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
HSA-MIR-320C-1 
           272 
AGE, nv=43, binary=FALSE, numeric=TRUE
HSA-MIR-23B 
        203 
GENDER, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-152 
        115 
KARNOFSKY.PERFORMANCE.SCORE, nv=6, binary=FALSE, numeric=TRUE
HSA-MIR-3613 
         303 
NUMBERPACKYEARSSMOKED, nv=30, binary=FALSE, numeric=TRUE
HSA-MIR-3682 
         330 
STOPPEDSMOKINGYEAR, nv=31, binary=FALSE, numeric=TRUE
HSA-MIR-548O 
         482 
TOBACCOSMOKINGHISTORYINDICATOR, nv=5, binary=FALSE, numeric=TRUE
HSA-MIR-765 
        551 
[1] "TOBACCOSMOKINGHISTORYINDICATOR"
[1] "num to class table"
vv1
 1  2  3  4  5 
23 20 30 22  2 
> q(save="no")
