
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-TP/4426113/LUAD-TP.meth.by_min_expr_corr.data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/LUAD-TP/4397267/LUAD-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=453, in expression file=435, common to both=391
Number of genes in original expression dataset=20000
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "COMPLETENESS.OF.RESECTION"             
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 391 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-05-4384 TCGA-05-4390 TCGA-05-4396 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 
         426         1126           NA          610           NA           NA 
TCGA-05-4417 TCGA-05-4424 TCGA-05-4425 TCGA-05-4427 TCGA-05-4433 TCGA-05-5420 
         454          913          669          791          730          457 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-5375 
         151          881          670           30           62          264 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 
         354         1357          448           NA          133         1429 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3917 TCGA-44-3918 TCGA-44-4112 
        1301           97          246         1183          715          722 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
         417          498          383          407          328          302 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
         845          362          165          370         1938           NA 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
        1110           NA          444          325          366          218 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
         557           NA          531          535          719          385 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
          98          260          392          202          287          337 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
         135          114           76           NA           NA           NA 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
         157         1700          457          369          890          521 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         354           NA           NA         2174         2146          455 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
         785          944         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           NA           NA          567 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
         882          764          686           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-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 
          NA           NA          424          280           87            2 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
         992           24           NA         1238           NA           28 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
        1475           NA           NA           NA           67           NA 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
          NA         1826           NA         1233         2161         1170 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
          61           18           34           NA            4           95 
TCGA-55-7576 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
          40           39           31           31           24           54 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
          31           19           16          197           21            3 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
          31            5           33           21           92            6 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8204 
          43           26            4           47           15           NA 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
          46           66          215           43           22           29 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
          11           NA          227            9            3          146 
TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
         212           15           48           49           65          105 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
          33           31           29           48           NA            1 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
          28            5           47          161           NA          705 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
         940           NA         2093         1444           NA           NA 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 
          NA           NA         1708         1630           NA          882 
TCGA-62-A472 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
         540         1685           NA         2676           62         1305 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
         864         1559          865           NA          173          140 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
         422          202          186          690          414          165 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
         230          184           70           89          382           99 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4676 
          76          128          214           61         1599          164 
TCGA-73-7498 TCGA-73-7499 TCGA-75-5122 TCGA-75-5125 TCGA-75-5126 TCGA-75-5146 
         621          519           NA           NA           NA           NA 
TCGA-75-5147 TCGA-75-6203 TCGA-75-6205 TCGA-75-6207 TCGA-75-6211 TCGA-75-6212 
          NA           NA           NA           NA           NA           NA 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7030 TCGA-75-7031 TCGA-78-7143 
          NA           NA           NA           NA           NA           NA 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
          NA           NA           NA           NA         1093           NA 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
        1201          760           NA           NA           NA           NA 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
        1220          678          214           NA         6812           NA 
TCGA-78-7167 TCGA-78-7220 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-78-8640 TCGA-78-8648 TCGA-78-8655 
         881           NA          994         6345           NA         2360 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-80-5611 TCGA-83-5908 
          NA           NA           NA           NA           NA          823 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
          NA           NA           11          630          422           NA 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
          34           NA          508          745           10           NA 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
          13           24           43           26           23           21 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
          16           NA           19           26           34           44 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
          33           17           15          454          404           10 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
          30           13           39          323           NA           60 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
         309           79          417          372          842          224 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
          35          492          196          173           36           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 
         218          297          127          185           34            2 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 
         163           21           40          132          123          963 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
        1965         1932         1331          775          181           NA 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
          22          106          181           NA           86          146 
TCGA-97-8179 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
          15          392          427          458           44          169 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
         153          113          287          282          238          212 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
          76          116            6          285          621          353 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
          NA           NA           NA           NA           NA           NA 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
          NA           NA           NA           NA           NA           NA 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK 
          NA           NA          142           NA           NA           NA 
TCGA-MP-A5C7 
        1490 
Variable 1:'AGE':	nDistinctValues=50,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=93,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=219,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=85,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=28,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "KARNOFSKY.PERFORMANCE.SCORE"           
 [8] "HISTOLOGICAL.TYPE"                     
 [9] "RADIATIONS.RADIATION.REGIMENINDICATION"
[10] "NUMBERPACKYEARSSMOKED"                 
[11] "YEAROFTOBACCOSMOKINGONSET"             
[12] "COMPLETENESS.OF.RESECTION"             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 391 columns, 1 survival variables, and 12 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
LARP1 
 9210 
AGE, nv=50, binary=FALSE, numeric=TRUE
LOC148696 
     9601 
NEOPLASM.DISEASESTAGE, nv=8, binary=FALSE, numeric=FALSE
 PAN2 
12356 
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
ACBD5 
  145 
[1] "PATHOLOGY.T.STAGE"
[1] "num to class table"
vv1
  1   2   3   4 
123 217  33  15 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
POLR2J3__1 
     13502 
[1] "PATHOLOGY.N.STAGE"
[1] "num to class table"
vv1
  0   1   2   3 
251  71  59   1 
PATHOLOGY.M.STAGE, nv=5, binary=FALSE, numeric=FALSE
PPP2R5B 
  13685 
GENDER, nv=2, binary=FALSE, numeric=FALSE
KIF4B 
 8968 
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
C9ORF11 
   2771 
HISTOLOGICAL.TYPE, nv=12, binary=FALSE, numeric=FALSE
DNAJC25-GNG10__1 
            5036 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
ZNF642 
 19793 
NUMBERPACKYEARSSMOKED, nv=85, binary=FALSE, numeric=TRUE
FAM128A__1 
      5889 
YEAROFTOBACCOSMOKINGONSET, nv=55, binary=FALSE, numeric=TRUE
ADH1C 
  329 
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
DDX52 
 4753 
> q(save="no")
