
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.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/GDAC_mRNA_Preprocess_Median/KIRC-TP/2282317/0.GDAC_mRNA_Preprocess_Median.Finished/KIRC-TP.medianexp.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/KIRC-TP/2172441/1.GDAC_clinicalDataPicker.Finished/KIRC-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=502, in expression file=72, common to both=72
Number of genes in original expression dataset=17814
[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] "HISTOLOGICALTYPE"                      
[12] "PATHOLOGICSPREAD(PT)"                  
[13] "PATHOLOGICSPREAD(PN)"                  
[14] "PATHOLOGICSPREAD(M)"                   
[15] "TUMORSTAGE"                            
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "BATCHNUMBER"                           

Input Data has 17 rows and 72 columns.

[1] "Batch" "17"   
[1] "Last Follow UP"
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
        1120         1436           16         1190          735         1493 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
        1491         1130         1508         1477         1105         1186 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3328 TCGA-A3-3329 TCGA-A3-3331 TCGA-A3-3335 
         751         1137          785          706         1485          664 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
        1043          944          137         1097         1385          910 
TCGA-A3-3352 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3372 
         561         1286         1559          319          872          735 
TCGA-A3-3374 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-AK-3426 
        1313          630          567          574          861          884 
TCGA-AK-3427 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3453 
        2566         1744         1423         1471         1217         1190 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B2-3923 
         683           46          369           40           NA          178 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4102 TCGA-B8-4143 TCGA-B8-4148 
         194           50          110           15          709          379 
TCGA-B8-4151 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-BP-4161 TCGA-BP-4162 
         279          255           19          226         2746         3074 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4167 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 
        2839          992         2718         1820         1924         2227 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
         431         2308         1998         1661         1792          336 
Variable 1:'AGE':	nDistinctValues=41,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=70,	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=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=72,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'PATHOLOGY.T':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'PATHOLOGY.N':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'PATHOLOGICSPREAD(M)':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TUMOR.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'BATCH.NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                 "GENDER"              "PATHOLOGY.T"        
[4] "PATHOLOGY.N"         "PATHOLOGICSPREAD(M)" "TUMOR.STAGE"        
[1] "TUMOR.?STAGE" "6"           
[1] "stage2"
vv
 1  2  3  4 
40 15 12  5 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 72 columns, 1 survival variables, and 6 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
HERC3 
13858 
AGE, nv=41, binary=FALSE, numeric=TRUE
COL18A1 
    173 
GENDER, nv=2, binary=FALSE, numeric=FALSE
DDX3Y 
 9655 
PATHOLOGY.T, nv=3, binary=FALSE, numeric=TRUE
TRIM11 
  9691 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
T1 T2 T3 
41 14 17 
PATHOLOGY.N, nv=2, binary=FALSE, numeric=TRUE
M6PRBP1 
   2037 
PATHOLOGICSPREAD(M), nv=2, binary=FALSE, numeric=FALSE
IGFBPL1 
  15539 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
TRIM11 
  9691 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
     40      15      12       5 
> q(save="no")
