
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/BLCA-TP/2401216/0.GDAC_MethylationPreprocess.Finished/BLCA-TP.meth.for_correlation.filtered_data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/BLCA-TP/2328320/1.GDAC_clinicalDataPicker.Finished/BLCA-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=114, in expression file=96, common to both=87
Number of genes in original expression dataset=17337
[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 87 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
          NA           NA          363           NA           NA           NA 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
          NA           NA           NA           NA           NA           NA 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-C4-A0F0 
          NA           NA          179          111           NA           59 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
          61           14           13           21           NA           NA 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
          NA           NA           NA           NA          219          166 
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-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-E5-A2PC TCGA-FD-A3B3 TCGA-FD-A3B4 
        1151          168           NA         1108          268          253 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
          NA          209           NA          336          272          242 
TCGA-FD-A3NA TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
         974           71          417         1884          806          172 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3I6 
          NA          997          525          214           NA           68 
TCGA-GC-A3RB TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GV-A3JV 
         137          234           64           95          177          133 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QG TCGA-GV-A3QH TCGA-GV-A3QI 
         160          187          173           NA          237          125 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
          46          204           NA 
Variable 1:'AGE':	nDistinctValues=43,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=58,	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=11,	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=27,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'STOPPEDSMOKINGYEAR':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=4,	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 87 columns, 1 survival variables, and 6 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
SEPT4 
13383 
AGE, nv=43, binary=FALSE, numeric=TRUE
PPFIA4 
 11713 
GENDER, nv=2, binary=FALSE, numeric=FALSE
KIF4B 
 7934 
KARNOFSKY.PERFORMANCE.SCORE, nv=6, binary=FALSE, numeric=TRUE
HIPK3 
 6817 
NUMBERPACKYEARSSMOKED, nv=27, binary=FALSE, numeric=TRUE
CRMP1 
 3791 
STOPPEDSMOKINGYEAR, nv=28, binary=FALSE, numeric=TRUE
TALDO1 
 14781 
TOBACCOSMOKINGHISTORYINDICATOR, nv=4, binary=FALSE, numeric=TRUE
C6ORF195 
    2313 
[1] "TOBACCOSMOKINGHISTORYINDICATOR"
[1] "num to class table"
vv1
 1  2  3  4 
20 18 26 17 
> q(save="no")
