
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/LUAD/2044238/0.GDAC_MethylationPreprocess.Finished/LUAD.meth.for_correlation.filtered_data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LUAD/2044090/1.GDAC_clinicalDataPicker.Finished/LUAD.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=220, in expression file=181, common to both=173
Number of genes in original expression dataset=17306
[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] "NUMBERPACKYEARSSMOKED"                 
[19] "STOPPEDSMOKINGYEAR"                    
[20] "TOBACCOSMOKINGHISTORYINDICATOR"        
[21] "YEAROFTOBACCOSMOKINGONSET"             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 173 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-05-4390 TCGA-05-4396 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 
        1126          303          610           NA           90          454 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 
         913           NA          730           31          151           NA 
TCGA-05-5429 TCGA-05-5715 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-5645 
          30           62          354         1357          158          208 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
         102          302          236          165           82         1938 
TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 TCGA-44-7670 TCGA-44-7671 
          NA           NA          298           50          531          535 
TCGA-44-7672 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4512 TCGA-49-4514 
         418           NA           NA           NA           NA         1314 
TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 
         457          395          150            1           NA           NA 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 
        1485          455          785         1499          245          267 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
        1091         2369          653          257          460          285 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
         135          373           NA           NA         1015           NA 
TCGA-50-7109 TCGA-53-7626 TCGA-53-7813 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
         255          970          418            2          992           24 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
          NA           28         1475           NA           NA           67 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-7281 
          NA           NA         1826         1233         2161           18 
TCGA-55-7283 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 
          34            4           95           40           39           31 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 
          24           54           19           16           21            3 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 
        1685           NA         2550            3          926         1202 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
          27           21          422          154          186          690 
TCGA-69-7764 TCGA-69-7765 TCGA-71-6725 TCGA-73-4658 TCGA-73-4676 TCGA-75-5122 
         414          129           61         1599          122           NA 
TCGA-75-5126 TCGA-75-5146 TCGA-75-5147 TCGA-75-6203 TCGA-75-6205 TCGA-75-6207 
          NA           NA           NA           NA           NA           NA 
TCGA-75-6211 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7030 
          NA           NA           NA           NA           NA           NA 
TCGA-75-7031 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
          NA           NA           NA           NA           NA         1093 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
          NA         1201          760           NA           NA           NA 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
          NA         1220          678          214           NA         6812 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
          NA           NA           NA           NA           NA          327 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-80-5607 TCGA-80-5608 TCGA-86-6562 
         881           NA          994           NA           NA           NA 
TCGA-86-6851 TCGA-86-7713 TCGA-86-7714 TCGA-91-6828 TCGA-91-6829 TCGA-91-6835 
          NA            7           NA           37           NA           35 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-93-7347 TCGA-93-7348 
          NA          819           28           31          297          127 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 
          34            2          163          963         1476         1331 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-99-7458 
         263          181           NA           22          250 
Variable 1:'AGE':	nDistinctValues=43,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=47,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=107,	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=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=9,	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=8,	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:'NUMBERPACKYEARSSMOKED':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'STOPPEDSMOKINGYEAR':	nDistinctValues=40,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=40,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=8,	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"                   
[11] "NUMBERPACKYEARSSMOKED"                 
[12] "STOPPEDSMOKINGYEAR"                    
[13] "TOBACCOSMOKINGHISTORYINDICATOR"        
[14] "YEAROFTOBACCOSMOKINGONSET"             
[1] "TUMOR.?STAGE" "8"           
[1] "stage2"
vv
 1  2  3  4 
89 36 36  7 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "5"          
[1] "PATHOLOGY.N" "6"          
Output Data has 173 columns, 1 survival variables, and 14 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
ANO9 
 664 
AGE, nv=43, binary=FALSE, numeric=TRUE
METT10D 
   9341 
GENDER, nv=2, binary=FALSE, numeric=FALSE
KIF4B 
 7949 
KARNOFSKY.PERFORMANCE.SCORE, nv=6, binary=FALSE, numeric=TRUE
 WDR4 
16377 
HISTOLOGICAL.TYPE, nv=9, binary=FALSE, numeric=FALSE
GLTSCR2 
   6234 
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
GAPDH 
 6019 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
T1 T2 T3 T4 
50 96 13 13 
PATHOLOGY.N, nv=3, binary=FALSE, numeric=TRUE
KLHDC9 
  8008 
[1] "PATHOLOGY.N"
[1] "num to class table"
vv1
 N0  N1  N2 
105  32  32 
PATHOLOGICSPREAD(M), nv=3, binary=FALSE, numeric=FALSE
C2ORF73 
   2155 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
PCDHGC4 
  11009 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
     89      36      36       7 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
LYPLA2P1 
    9009 
NEOADJUVANT.THERAPY, nv=2, binary=FALSE, numeric=FALSE
FXYD5 
 5930 
NUMBERPACKYEARSSMOKED, nv=55, binary=FALSE, numeric=TRUE
CNTD2 
 3558 
STOPPEDSMOKINGYEAR, nv=40, binary=FALSE, numeric=TRUE
 SHBG 
13562 
TOBACCOSMOKINGHISTORYINDICATOR, nv=4, binary=FALSE, numeric=FALSE
CHRM1 
 3315 
YEAROFTOBACCOSMOKINGONSET, nv=40, binary=FALSE, numeric=TRUE
SERPINA1 
   13386 
> q(save="no")
