
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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_MethylationPreprocess/LUAD/1705805/0.GDAC_MethylationPreprocess.Finished/LUAD.meth.for_correlation.filtered_data.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=220, common to both=216
Number of genes in original expression dataset=20231
[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 216 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-05-4384 TCGA-05-4390 TCGA-05-4396 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 
         426         1126          303          610           NA           90 
TCGA-05-4417 TCGA-05-4424 TCGA-05-4425 TCGA-05-4427 TCGA-05-4433 TCGA-05-5420 
         454          913           NA          791          730           31 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-5375 
         151           90           NA           30           62          264 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-44-5643 TCGA-44-5644 
         354         1357          158           NA          106          498 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
         208            9          102          302          236           95 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
         165           82         1938           NA         1110           NA 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
         298          162          153           50          557           NA 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
         531          535          418           NA           NA           NA 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
          NA         1314          457          369          395          150 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
           1           NA           NA         2174         1485          455 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
         785          297         1499          245          282          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-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
         135          373          349           NA           NA           NA 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
          NA           NA           NA         1015           NA          255 
TCGA-53-7624 TCGA-53-7626 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
        1068          970           87            2          992           24 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
          NA         1238           NA           28         1475           NA 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
          NA           NA           67           NA           NA         1826 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
          NA         1233         2161         1170           61           18 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 
          34           NA            4           95           40           39 
TCGA-55-7727 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
          31           31           19           16          197           21 
TCGA-55-7914 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
           3         1685           NA         2550            3          926 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
         507         1145          223           NA           27           21 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
         422          154          186          690          414          129 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4676 TCGA-75-5122 TCGA-75-5125 TCGA-75-5126 
          61         1599          122           NA           NA           NA 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6203 TCGA-75-6205 TCGA-75-6207 TCGA-75-6211 
          NA           NA           NA           NA           NA           NA 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7030 TCGA-75-7031 
          NA           NA           NA           NA           NA           NA 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 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-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
          NA           NA           NA           NA           NA           NA 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-80-5607 TCGA-80-5608 
         327          881           NA          994           NA           NA 
TCGA-80-5611 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
          NA           NA           NA           11           27            7 
TCGA-86-7714 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
          NA           37           NA            1           39           35 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
          11           NA          819          127           28           31 
TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-97-7546 TCGA-97-7547 
         127           34            2          163          963         1435 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-99-7458 
        1476         1331          263          181           NA          250 
Variable 1:'AGE':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=128,	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=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'PATHOLOGY.T':	nDistinctValues=9,	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:'BATCH.NUMBER':	nDistinctValues=7,	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 
107  47  46  11 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "5"          
[1] "PATHOLOGY.N" "6"          
Output Data has 216 columns, 1 survival variables, and 10 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
TM4SF19 
  17924 
AGE, nv=44, binary=FALSE, numeric=TRUE
UGT3A1 
 18941 
GENDER, nv=2, binary=FALSE, numeric=FALSE
KIF4B 
 8666 
KARNOFSKY.PERFORMANCE.SCORE, nv=6, binary=FALSE, numeric=TRUE
KCNIP1 
  8391 
HISTOLOGICAL.TYPE, nv=11, binary=FALSE, numeric=FALSE
GOPC 
6906 
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
STK32A 
 17272 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
 T1  T2  T3  T4 
 60 125  17  12 
PATHOLOGY.N, nv=3, binary=FALSE, numeric=TRUE
ANXA6 
  730 
[1] "PATHOLOGY.N"
[1] "num to class table"
vv1
 N0  N1  N2 
125  44  42 
PATHOLOGICSPREAD(M), nv=3, binary=FALSE, numeric=FALSE
C3ORF58 
   2395 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
 RGS1 
14842 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
    107      47      46      11 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
 BBX 
1323 
NEOADJUVANT.THERAPY, nv=2, binary=FALSE, numeric=FALSE
MYADM 
11504 
> q(save="no")
