
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/COADREAD-TP/2401449/0.GDAC_MethylationPreprocess.Finished/COADREAD-TP.meth.for_correlation.filtered_data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/COADREAD-TP/2330187/1.GDAC_clinicalDataPicker.Finished/COADREAD-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=588, in expression file=37, common to both=35
Number of genes in original expression dataset=16969
[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] "HISTOLOGICALTYPE"                      
[11] "PATHOLOGICSPREAD(PT)"                  
[12] "PATHOLOGICSPREAD(PN)"                  
[13] "PATHOLOGICSPREAD(M)"                   
[14] "TUMORSTAGE"                            
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 35 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 
         595          522          552          424          387          464 
TCGA-A6-4107 TCGA-AA-3488 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
         231           91           NA           31           31           31 
TCGA-AA-3506 TCGA-AA-3509 TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 
          NA           NA         1714          957         1334          172 
TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-CA-5256 TCGA-CK-4951 TCGA-CM-4746 
         505         2180         1705           NA         1491          699 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-AG-A01W 
         244          214          244          123          183         2130 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A036 
        1946          334           59         1884         2192 
Variable 1:'AGE':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=29,	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=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
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=29,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'PATHOLOGY.T':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'PATHOLOGY.N':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'PATHOLOGICSPREAD(M)':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                     "PRIMARY.SITE.OF.DISEASE"
[3] "GENDER"                  "HISTOLOGICAL.TYPE"      
[5] "PATHOLOGY.T"             "PATHOLOGY.N"            
[7] "PATHOLOGICSPREAD(M)"     "TUMOR.STAGE"            
[1] "TUMOR.?STAGE" "8"           
[1] "stage2"
vv
 1  2  3  4 
 6 13  7  5 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "5"          
[1] "PATHOLOGY.N" "6"          
Output Data has 35 columns, 1 survival variables, and 8 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
ELAVL3 
  4727 
AGE, nv=23, binary=FALSE, numeric=TRUE
PTCHD2 
 11765 
PRIMARY.SITE.OF.DISEASE, nv=2, binary=FALSE, numeric=FALSE
HAGH 
6489 
GENDER, nv=2, binary=FALSE, numeric=FALSE
AMPD1 
  537 
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
C4ORF38 
   2163 
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
DSC3 
4453 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
T1 T2 T3 T4 
 2  6 22  5 
PATHOLOGY.N, nv=3, binary=FALSE, numeric=TRUE
FBXO33 
  5390 
[1] "PATHOLOGY.N"
[1] "num to class table"
vv1
N0 N1 N2 
22 10  3 
PATHOLOGICSPREAD(M), nv=3, binary=FALSE, numeric=FALSE
THAP11 
 14716 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
WBSCR17 
  16029 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
      6      13       7       5 
> q(save="no")
