
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
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-TM/3141126/0.GDAC_MethylationPreprocess.Finished/SKCM-TM.meth.for_correlation.filtered_data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/SKCM-TM/3132753/1.GDAC_clinicalDataPicker.Finished/SKCM-TM.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=177, in expression file=241, common to both=168
Number of genes in original expression dataset=17129
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "RADIATIONTHERAPY"                      
[10] "RADIATIONS.RADIATION.REGIMENINDICATION"
[11] "DISTANT.METASTASIS"                    
[12] "LYMPH.NODE.METASTASIS"                 
[13] "TUMOR.STAGECODE"                       
[14] "NEOPLASM.DISEASESTAGE"                 
[15] "BATCHNUMBER"                           

Input Data has 15 rows and 168 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
        3687           NA           NA           NA           NA           NA 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE 
          NA         1483           NA           NA         2167           NA 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
          NA           NA          653         4511         1513           82 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
         194          345           98         1487           NA         3564 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
          NA         5926           NA           NA         3265         1861 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F5 
          NA           NA          713           NA           NA         6553 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
         477           NA           NA           NA           NA           NA 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
          NA         3335         2399           NA           NA         1455 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
          NA         1205          979           NA         1349           NA 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
        1716         1136          440         1700        10523           NA 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
          NA           NA         2401          743           NA         1787 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
        1446         1315         9567         4134         5536          686 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
        2717         1664         1673         2296         2766         3101 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
          NA          435         1691          595         2042           NA 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
        3931           NA           NA           NA           NA           NA 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
          NA           NA           NA           NA         4403         6175 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
          NA           NA         7562           NA         3150         4150 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
        1265         1620          129         3733          786          112 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19D TCGA-ER-A19F 
         813           NA          714           NA           NA           NA 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19O TCGA-ER-A1A1 
          NA           NA           NA         1340           NA         2433 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A3YO TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YX 
        1010         2448           NA         4885           NA           NA 
TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG 
          NA           NA           NA         1225           NA           NA 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ 
          NA           NA           NA         3080           NA           NA 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY 
          NA         4525         1617           NA         1505           NA 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 
          NA         2366           NA          378         1504            6 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 
         699         1446           NA           NA         3664           NA 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
        2577           NA           NA           NA           NA         1204 
Variable 1:'AGE':	nDistinctValues=63,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=83,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=81,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'DISTANT.METASTASIS':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'LYMPH.NODE.METASTASIS':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'TUMOR.STAGECODE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'NEOPLASM.DISEASESTAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH.NUMBER':	nDistinctValues=5,	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 TIS  TX 
  6   4  14   2  18  16   6   4  21  13   4   6  27   1  11 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 168 columns, 1 survival variables, and 7 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
NR4A3 
10338 
AGE, nv=63, binary=FALSE, numeric=TRUE
ITGA8 
 7427 
PRIMARY.SITE.OF.DISEASE, nv=4, binary=FALSE, numeric=FALSE
DAZAP1 
  4032 
GENDER, nv=2, binary=FALSE, numeric=FALSE
DDX43 
 4141 
DISTANT.METASTASIS, nv=5, binary=FALSE, numeric=FALSE
 SELT 
13202 
LYMPH.NODE.METASTASIS, nv=10, binary=FALSE, numeric=FALSE
NGLY1 
10127 
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
[1] "Clinical variable TUMOR.STAGECODE has too few non-missing values, n=0"
NEOPLASM.DISEASESTAGE, nv=13, binary=FALSE, numeric=FALSE
  TTN 
15692 
> q(save="no")
