
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/LUSC-TP/2662149/0.GDAC_MethylationPreprocess.Finished/LUSC-TP.meth.for_correlation.filtered_data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LUSC-TP/2587688/1.GDAC_clinicalDataPicker.Finished/LUSC-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=324, in expression file=130, common to both=130
Number of genes in original expression dataset=17543
[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] "NUMBERPACKYEARSSMOKED"                 
[18] "STOPPEDSMOKINGYEAR"                    
[19] "TOBACCOSMOKINGHISTORYINDICATOR"        
[20] "YEAROFTOBACCOSMOKINGONSET"             
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 130 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-18-3417 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-5782 TCGA-21-5783 
         758         2753           92          826          962           NA 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-4593 TCGA-22-4599 TCGA-22-4601 
         908          656          329         1067         1161         1057 
TCGA-22-4605 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
          NA          358          964         1974         1932          444 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
        1345           24         1651         2170           NA          357 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4566 
         573          915         1912         1713          505         5286 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6737 TCGA-33-6738 
        3149         4299          428           NA           NA          821 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
        1528         1575          994           NA          329          235 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-37-5819 
         428          698          168           NA           NA          103 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 
        1454         2253         1360         2086         2130         1848 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
          52          740           59          832         1107          474 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 
        1084           24          544          258          213          183 
TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-46-6025 TCGA-46-6026 TCGA-51-6867 
          85           NA          212           29           18           NA 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 
           3           NA           62           31           30           13 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7822 TCGA-60-2703 
          30           44           40           26            1           NA 
TCGA-60-2704 TCGA-60-2709 TCGA-63-5128 TCGA-63-5131 TCGA-63-6202 TCGA-63-7020 
          NA         1505           NA           NA           NA           NA 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 
          NA           NA           NA           NA           NA           NA 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 
          NA           NA           NA           NA         2736           NA 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
          15         1285           NA           NA           NA           NA 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-79-5596 TCGA-85-6175 
         479           NA           NA         1641           NA           NA 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 
          11           24           34           NA           38           60 
TCGA-90-6837 TCGA-90-7964 TCGA-92-7340 TCGA-92-7341 TCGA-94-7033 TCGA-94-7557 
          41          100           82          106           87           NA 
TCGA-94-7943 TCGA-96-7544 TCGA-96-7545 TCGA-98-7454 
         143         1213         1777          115 
Variable 1:'AGE':	nDistinctValues=36,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=88,	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=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'PATHOLOGY.T':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'PATHOLOGY.N':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'PATHOLOGICSPREAD(M)':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TUMOR.STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBERPACKYEARSSMOKED':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'STOPPEDSMOKINGYEAR':	nDistinctValues=32,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=36,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=9,	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] "NUMBERPACKYEARSSMOKED"                 
[11] "STOPPEDSMOKINGYEAR"                    
[12] "TOBACCOSMOKINGHISTORYINDICATOR"        
[13] "YEAROFTOBACCOSMOKINGONSET"             
[1] "TUMOR.?STAGE" "8"           
[1] "stage2"
vv
 1  2  3  4 
67 39 20  1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "5"          
[1] "PATHOLOGY.N" "6"          
Output Data has 130 columns, 1 survival variables, and 13 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
GRIK4 
 6576 
AGE, nv=36, binary=FALSE, numeric=TRUE
 EVC 
5141 
GENDER, nv=2, binary=FALSE, numeric=FALSE
KIF4B 
 8032 
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
NDUFB2 
 10281 
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
CAB39L 
  2548 
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
 VAV1 
16462 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
T1 T2 T3 T4 
33 79 14  4 
PATHOLOGY.N, nv=3, binary=FALSE, numeric=TRUE
MST1P9 
  9872 
[1] "PATHOLOGY.N"
[1] "num to class table"
vv1
N0 N1 N2 
83 36 10 
PATHOLOGICSPREAD(M), nv=3, binary=FALSE, numeric=FALSE
 CR2 
3798 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
RAP1GDS1 
   12548 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
     67      39      20       1 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
PHACTR3 
  11403 
NUMBERPACKYEARSSMOKED, nv=48, binary=FALSE, numeric=TRUE
ADH1B 
  292 
STOPPEDSMOKINGYEAR, nv=32, binary=FALSE, numeric=TRUE
C6ORF162 
    2341 
TOBACCOSMOKINGHISTORYINDICATOR, nv=4, binary=FALSE, numeric=FALSE
TP53I3 
 15760 
YEAROFTOBACCOSMOKINGONSET, nv=36, binary=FALSE, numeric=TRUE
KDM4C 
 7856 
> q(save="no")
