
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.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-Regional_Metastatic/3155027/0.GDAC_RPPA_preprocess.Finished/SKCM-Regional_Metastatic.rppa.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-Regional_Metastatic/3215667/SKCM-Regional_Metastatic.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=152, in expression file=95, common to both=95
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 95 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
          NA           NA           NA         3687           NA           NA 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-D9-A148 TCGA-D9-A149 
          NA           NA           NA           NA         4511         1513 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
          82          194         1487           NA         3564           NA 
TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 
          NA           NA          713           NA           NA           NA 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
          NA         2399         1455         1205          979           NA 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A0 
          NA         1716          440         1700        10523           NA 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK 
         743         1787         1315         5536          686         1664 
TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
        1673           NA          435         1691          595         2042 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MI 
          NA         3931           NA           NA           NA           NA 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
          NA         4403         6175           NA           NA         7562 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
        3150         4150         1265         1620          129         3733 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-ER-A19D 
         786          112          813           NA          714           NA 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19O TCGA-ER-A1A1 
          NA           NA           NA         1340           NA         2433 
TCGA-FS-A1YW TCGA-FS-A1Z4 TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        3080           NA           NA         3664           NA         2577 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
          NA           NA           NA           NA         1204 
Variable 1:'AGE':	nDistinctValues=47,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=47,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=47,	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=2,	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=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=13,	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 
  3   3   9   3   9   6   2   3  13   5   3   3  12   8 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 95 columns, 1 survival variables, and 7 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
GSK3A GSK3B|GSK3-ALPHA-BETA-M-V 
                             66 
AGE, nv=47, binary=FALSE, numeric=TRUE
SHC1|SHC_PY317-R-C 
               126 
PRIMARY.SITE.OF.DISEASE, nv=2, binary=FALSE, numeric=FALSE
BCL2L11|BIM-R-V 
             28 
GENDER, nv=2, binary=FALSE, numeric=FALSE
SRC|SRC-M-V 
        132 
DISTANT.METASTASIS, nv=4, binary=FALSE, numeric=FALSE
C12ORF5|TIGAR-R-V 
              140 
LYMPH.NODE.METASTASIS, nv=9, binary=FALSE, numeric=FALSE
ESR1|ER-ALPHA-R-V 
               56 
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
BIRC2 |CIAP-R-V 
            160 
> q(save="no")
