
R version 2.10.1 (2009-12-14)
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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.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/SKCM-BRAF_Hotspot_Mutants/3155607/0.GDAC_MethylationPreprocess.Finished/SKCM-BRAF_Hotspot_Mutants.meth.for_correlation.filtered_data.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=64, in expression file=99, common to both=64
Number of genes in original expression dataset=17172
[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 64 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE 
          NA           NA           NA           NA           NA           NA 
TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
          NA           NA           NA           NA         1555           NA 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
          NA           NA         1354         1116           NA          534 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
         451           NA         1097          156           NA           NA 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T 
        1155         1175          134          825          366          197 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT 
         272           NA           NA           NA           NA           NA 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J TCGA-ER-A19O TCGA-FS-A1YX TCGA-FS-A1YY 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
          NA           NA          756         2577 
Variable 1:'AGE':	nDistinctValues=43,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=33,	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=22,	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=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=3,	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  T2 T2A T2B  T3 T3A T3B T4A T4B TIS  TX 
  2   1   5  11   6   2   2   7   3   2  10   1   6 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 64 columns, 1 survival variables, and 7 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
PPARG 
11606 
AGE, nv=43, binary=FALSE, numeric=TRUE
MRAS 
9508 
PRIMARY.SITE.OF.DISEASE, nv=4, binary=FALSE, numeric=FALSE
 PSPN 
11972 
GENDER, nv=2, binary=FALSE, numeric=FALSE
FRAT1 
 5778 
DISTANT.METASTASIS, nv=5, binary=FALSE, numeric=FALSE
MUL1 
9722 
LYMPH.NODE.METASTASIS, nv=9, binary=FALSE, numeric=FALSE
 TGM4 
14887 
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
[1] "Clinical variable TUMOR.STAGECODE has too few non-missing values, n=0"
NEOPLASM.DISEASESTAGE, nv=12, binary=FALSE, numeric=FALSE
C4ORF3 
  2194 
> q(save="no")
