
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_RPPA_preprocess/SKCM-BRAF_Hotspot_Mutants/3154955/0.GDAC_RPPA_preprocess.Finished/SKCM-BRAF_Hotspot_Mutants.rppa.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-BRAF_Hotspot_Mutants/3215664/SKCM-BRAF_Hotspot_Mutants.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=67, in expression file=63, common to both=42
Number of genes in original expression dataset=175
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "DAYSTOSUBMITTEDSPECIMENDX"             
 [5] "VITALSTATUS"                           
 [6] "DCCUPLOADDATE"                         
 [7] "PRIMARYSITEOFDESEASE"                  
 [8] "GENDER"                                
 [9] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[10] "RADIATIONTHERAPY"                      
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "DISTANT.METASTASIS"                    
[13] "LYMPH.NODE.METASTASIS"                 
[14] "TUMOR.STAGECODE"                       
[15] "NEOPLASM.DISEASESTAGE"                 
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 42 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3CE 
          NA           NA         3004           NA           NA           NA 
TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 
          NA           NA           NA         1555           NA           NA 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
        1354           NA          156         1155         1175          134 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GH TCGA-EE-A2GS 
         825          366          197          272           NA           NA 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MK TCGA-EE-A2MP 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-ER-A19J TCGA-ER-A19O 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-GN-A262 TCGA-GN-A265 
          NA           NA           NA           NA          756         2577 
Variable 1:'AGE':	nDistinctValues=33,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=24,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 6:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                     "PRIMARY.SITE.OF.DISEASE"
[3] "GENDER"                  "DISTANT.METASTASIS"     
[5] "LYMPH.NODE.METASTASIS"   "TUMOR.STAGECODE"        
[7] "NEOPLASM.DISEASESTAGE"  
[1] "TUMOR.?STAGE" "6"           
[1] "stage2"
vv
 T0  T1 T1A T1B  T2 T2A T2B  T3 T3A T3B  T4 T4A T4B  TX 
  1   1   4   1   4   4   1   1   4   2   1   1   5   6 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 42 columns, 1 survival variables, and 7 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
C12ORF5|TIGAR-R-V 
              140 
AGE, nv=33, binary=FALSE, numeric=TRUE
SHC1|SHC_PY317-R-C 
               126 
PRIMARY.SITE.OF.DISEASE, nv=4, binary=FALSE, numeric=FALSE
RPS6|S6-R-C 
        120 
GENDER, nv=2, binary=FALSE, numeric=FALSE
ATM|ATM-R-C 
         15 
DISTANT.METASTASIS, nv=4, binary=FALSE, numeric=FALSE
PTK2|FAK-R-C 
          60 
LYMPH.NODE.METASTASIS, nv=8, binary=FALSE, numeric=FALSE
BCL2L1|BCL-XL-R-V 
               25 
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
[1] "Clinical variable TUMOR.STAGECODE has too few non-missing values, n=0"
NEOPLASM.DISEASESTAGE, nv=11, binary=FALSE, numeric=FALSE
INPP4B|INPP4B-G-C 
               76 
> q(save="no")
