
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/LUAD/2008588/0.mRNAseq_preprocessor.Finished/LUAD.uncv2.mRNAseq_RSEM_normalized_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LUAD/1971864/1.GDAC_clinicalDataPicker.Finished/LUAD.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=294, in expression file=353, common to both=286
Number of genes in original expression dataset=18330
[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 286 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-05-4244 TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 
          NA         1158          121          606          426           NA 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 
        1126           NA          303           NA         1431           NA 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 
          NA          610           NA           90          454           NA 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
         911           NA          913           NA          791          791 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
         761          761          730          457           31          151 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
          90           NA           30           62           14          224 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
         181          264         1448         2595         1147         1491 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
         863         1073          354         1357          158           NA 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 
         574          581          400          529          103          480 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
         400           97          246          311          253          196 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 
         189          140          106          498          208          102 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
         302          236           95          165           82         1938 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
          NA         1110           NA          298          162          153 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
          50          557           NA          531          535          418 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
        2318           NA           NA           NA         1081         1421 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
         428          999          268          896           NA         1314 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
         457          369          395          150            1           NA 
TCGA-50-5044 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
          NA         1485          455          785          297         1499 
TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
         245          267         1091         2369          653          257 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
         460          285          135          373          349           NA 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
          NA           NA           NA           NA           NA         1015 
TCGA-50-6673 TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 
          NA          255         1068          970          418          701 
TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        1178         1479         1374           87            2          992 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
          24           NA         1238           NA           28         1475 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
          NA           NA           NA           67           NA           NA 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
        1826           NA         1233         2161         1170           61 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
          18           34           NA            4           95           40 
TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
          39           31           24           54           19           16 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 
         197           21            3         1728          628         1189 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
        1685         1126           NA         2550            3          926 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
         507         1202          223           30           60           18 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
          62           18           NA           27           21          422 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-71-6725 
         154          186          690          414          129           61 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        1599          711          911          617          467           14 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-75-5122 TCGA-75-5125 TCGA-75-5126 
          40          122           38           NA           NA           NA 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6203 TCGA-75-6205 TCGA-75-6206 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-78-7146 TCGA-78-7147 TCGA-78-7148 
          NA           NA           NA           NA           NA           NA 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
        1093           NA         1201          760           NA           NA 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
          NA           NA         1220          678          214           NA 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
        6812           NA           NA           NA           NA           NA 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-80-5607 
          NA          327          881           NA          994           NA 
TCGA-80-5608 TCGA-80-5611 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
          NA           NA          420           NA           NA           11 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
          27            7           NA           37           NA            1 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
          39           35           11           NA          819          127 
TCGA-91-6849 TCGA-91-7771 TCGA-93-7347 TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 
          28           31          297          127           34            2 
TCGA-95-7567 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         163          963         1435         1476         1331          263 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-99-7458 
         181           NA           22          250 
Variable 1:'AGE':	nDistinctValues=47,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=78,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=174,	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=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=71,	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=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=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=11,	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 
147  61  57  16 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "5"          
[1] "PATHOLOGY.N" "6"          
Output Data has 286 columns, 1 survival variables, and 10 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
ESYT3|83850 
       5341 
AGE, nv=47, binary=FALSE, numeric=TRUE
C11ORF84|144097 
           1669 
GENDER, nv=2, binary=FALSE, numeric=FALSE
PRKY|5616 
    12612 
KARNOFSKY.PERFORMANCE.SCORE, nv=6, binary=FALSE, numeric=TRUE
GTF3C6|112495 
         6976 
HISTOLOGICAL.TYPE, nv=11, binary=FALSE, numeric=FALSE
A4GNT|51146 
         25 
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
FAM125B|89853 
         5502 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
 T1  T2  T3  T4 
 79 167  23  16 
PATHOLOGY.N, nv=4, binary=FALSE, numeric=TRUE
RARS|5917 
    13126 
[1] "PATHOLOGY.N"
[1] "num to class table"
vv1
 N0  N1  N2  N3 
171  58  50   1 
PATHOLOGICSPREAD(M), nv=3, binary=FALSE, numeric=FALSE
C19ORF10|56005 
          1942 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
ZNF540|163255 
        18040 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
    147      61      57      16 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
LRTM2|654429 
        9464 
NEOADJUVANT.THERAPY, nv=2, binary=FALSE, numeric=FALSE
MSH4|4438 
    10290 
> q(save="no")
