
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/miRseq_preprocessor/LUAD/1676792/0.miRseq_preprocessor.Finished/LUAD.miRseq_RPKM_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LUAD/1669676/1.GDAC_clinicalDataPicker.Finished/LUAD.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=292, in expression file=100, common to both=100
Number of genes in original expression dataset=524
[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] "KARNOFSKYPERFORMANCESCORE"             
[11] "HISTOLOGICALTYPE"                      
[12] "PATHOLOGICSPREAD(PT)"                  
[13] "PATHOLOGICSPREAD(PN)"                  
[14] "PATHOLOGICSPREAD(M)"                   
[15] "TUMORSTAGE"                            
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "NEOADJUVANTTHERAPY"                    
[18] "BATCHNUMBER"                           

Input Data has 18 rows and 100 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-05-4244 TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4389 TCGA-05-4395 
          NA         1158          121          606           NA           NA 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4418 TCGA-05-4420 
          NA         1431           NA           NA           NA          911 
TCGA-05-4422 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4434 TCGA-35-3615 
          NA          791          761          761          457           14 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
         224          181         1448         2595         1147         1491 
TCGA-38-4629 TCGA-38-4630 TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
         863         1073          574          581          400          529 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
         103          480          400           97          246          311 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-49-4486 
         253          196          189          140          106         2318 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
        1081         1421          428          999          268          896 
TCGA-49-6761 TCGA-50-5936 TCGA-50-5939 TCGA-50-6673 TCGA-55-1592 TCGA-55-1594 
           1          257          460           NA          701         1178 
TCGA-55-1595 TCGA-55-1596 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
        1479         1374           NA         1238           NA           28 
TCGA-55-6972 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        1475           NA           NA           67           NA           NA 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-64-1676 
        1826           NA         1233         2161         1170         1728 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
         628         1189         1126          223           30           60 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-73-4659 TCGA-73-4662 TCGA-73-4675 
          18           62           18          711          911           40 
TCGA-75-5146 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7030 TCGA-75-7031 
          NA           NA           NA           NA           NA           NA 
TCGA-80-5607 TCGA-80-5608 TCGA-86-6851 TCGA-91-6830 TCGA-91-6840 TCGA-91-6847 
          NA           NA           NA            1           NA          819 
TCGA-91-6848 TCGA-91-6849 TCGA-95-7039 TCGA-95-7043 
         127           28           34            2 
Variable 1:'AGE':	nDistinctValues=35,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=69,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'PATHOLOGY.T':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'PATHOLOGY.N':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'PATHOLOGICSPREAD(M)':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TUMOR.STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "GENDER"                                
 [3] "KARNOFSKY.PERFORMANCE.SCORE"           
 [4] "HISTOLOGICAL.TYPE"                     
 [5] "PATHOLOGY.T"                           
 [6] "PATHOLOGY.N"                           
 [7] "PATHOLOGICSPREAD(M)"                   
 [8] "TUMOR.STAGE"                           
 [9] "RADIATIONS.RADIATION.REGIMENINDICATION"
[10] "NEOADJUVANT.THERAPY"                   
[1] "TUMOR.?STAGE" "8"           
[1] "stage2"
vv
 1  2  3  4 
53 24 19  4 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "5"          
[1] "PATHOLOGY.N" "6"          
Output Data has 100 columns, 1 survival variables, and 10 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
HSA-MIR-582 
        448 
AGE, nv=35, binary=FALSE, numeric=TRUE
HSA-MIR-653 
        474 
GENDER, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-99A 
        523 
KARNOFSKY.PERFORMANCE.SCORE, nv=4, binary=FALSE, numeric=TRUE
HSA-MIR-138-2 
           86 
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "num to class table"
vv1
  0  80  90 100 
  1   1   3   1 
HISTOLOGICAL.TYPE, nv=6, binary=FALSE, numeric=FALSE
HSA-MIR-369 
        311 
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
HSA-MIR-340 
        270 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
T1 T2 T3 T4 
27 62  8  3 
PATHOLOGY.N, nv=4, binary=FALSE, numeric=TRUE
HSA-MIR-3662 
         300 
[1] "PATHOLOGY.N"
[1] "num to class table"
vv1
N0 N1 N2 N3 
58 22 17  1 
PATHOLOGICSPREAD(M), nv=3, binary=FALSE, numeric=FALSE
HSA-MIR-106B 
          21 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
HSA-MIR-1293 
          66 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
     53      24      19       4 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-580 
        446 
NEOADJUVANT.THERAPY, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-3200 
         247 
> q(save="no")
