
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/mRNAseq_preprocessor/CESC-TP/4401812/CESC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/CESC-TP/4395285/CESC-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=74, in expression file=145, common to both=63
Number of genes in original expression dataset=18202
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "HISTOLOGICALTYPE"                      
[14] "RADIATIONS.RADIATION.REGIMENINDICATION"
[15] "NUMBERPACKYEARSSMOKED"                 
[16] "NUMBER.OF.LYMPH.NODES"                 
[17] "BATCHNUMBER"                           

Input Data has 17 rows and 63 columns.

[1] "Batch" "17"   
[1] "Last Follow UP"
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN 
        1505          925           NA         1112         5385           NA 
TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY 
          NA         1616           NA           NA           NA         2382 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
        2669         1791           NA           81         2127         2892 
TCGA-DS-A1OB TCGA-DS-A1OC TCGA-DS-A1OD TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-EA-A1QT 
          NA          376         3096          183          208            8 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EA-A439 
          53           40           25           19           81           20 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-EX-A1H6 
           9           10            8           NA          500          241 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
          37           37           30           66            2           31 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
          44           48           45           24          106           41 
TCGA-FU-A57G TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LA 
          31          773           NA          244         4482         3780 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LK TCGA-IR-A3LL 
          NA         3571         2948         2393          808         1106 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
         904            2          132 
Variable 1:'AGE':	nDistinctValues=35,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBERPACKYEARSSMOKED':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'BATCH.NUMBER':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "PATHOLOGY.T.STAGE"                     
[3] "PATHOLOGY.N.STAGE"                     
[4] "PATHOLOGY.M.STAGE"                     
[5] "HISTOLOGICAL.TYPE"                     
[6] "RADIATIONS.RADIATION.REGIMENINDICATION"
[7] "NUMBERPACKYEARSSMOKED"                 
[8] "NUMBER.OF.LYMPH.NODES"                 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "2"          
[1] "PATHOLOGY.N" "3"          
Output Data has 63 columns, 1 survival variables, and 8 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
CARNS1|57571 
        2735 
AGE, nv=35, binary=FALSE, numeric=TRUE
CMA1|1215 
     3638 
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
CHRM4|1132 
      3448 
[1] "PATHOLOGY.T.STAGE"
[1] "num to class table"
vv1
 1  2  3  4 
40 17  1  1 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
AKAP14|158798 
          451 
PATHOLOGY.M.STAGE, nv=2, binary=FALSE, numeric=FALSE
SBDSP1|155370 
        13839 
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
PDZD3|79849 
      11707 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
FAM116A|201627 
          5430 
NUMBERPACKYEARSSMOKED, nv=11, binary=FALSE, numeric=TRUE
MCTP2|55784 
       9733 
NUMBER.OF.LYMPH.NODES, nv=6, binary=FALSE, numeric=TRUE
TMEM229B|161145 
          16097 
> q(save="no")
