[1] "libdir: /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/ClinicalAnalysisAllGenes_new/broadinstitute.org/cancer.genome.analysis/00333/60/"
[1] "terrence_modification_tag: TRUE"
[1] "op: "
[1] "dfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/LUAD-TP/11494003/LUAD-TP.meth.by_min_clin_corr.data.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LUAD-TP/11541582/LUAD-TP.merged_data.txt"
[1] "gv: ALL"
[1] "gfn: "
[1] "sfn: "
[1] "fv: ALL"
[1] "ofn: "
[1] "dx: "
[1] "cfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LUAD-TP/11541582/LUAD-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=483, in expression file=449, common to both=417
Number of genes in original expression dataset=19984
[1] "ALL"
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [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] "RACE"                                  
[22] "ETHNICITY"                             
[23] "BATCHNUMBER"                           

Input Data has 23 rows and 417 columns.

[1] "Batch" "23"   
[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 
         455          913          669          791          730          457 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-5375 
         151          882          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         1036          722 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
        1013          863          383          723          328          302 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
         845          704          658          705         1938           NA 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
        1864           NA          444          592          366          218 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
         557           NA          882          535          719          385 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
          99          260          486          466          287          337 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
         351          415           76           NA           NA           NA 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
         157         1700          445          369          890          522 
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          246          282          267 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
        1091         2370          653           NA           NA          567 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
         883          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-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 
         105           NA           NA          424          280           87 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
           2          993           24           NA         1239           NA 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
          25         1475           NA           NA           NA           67 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
          NA           NA         1826           NA         1233         2151 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
        1170           53           18           35          121            6 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
           4           95           40          705           39           39 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
          34           24           54           44           19           16 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
         197           21            3           31            5           33 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
         462          100            6          600           26            4 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8204 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
          47           15           NA           33           46           66 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
         674          216           44           23           29           11 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
           8           15          228            9            3          146 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
         202          536           15           48           49           66 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
         106           33           42           29           48           NA 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
           1           28            5           47          162           NA 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
        1216         1289           NA         2696         1445           NA 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
          NA           NA           NA         2067         2199           NA 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
          NA         1246          910         1686           NA         2676 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-4679 
          62         1305          864         1559          866           NA 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
         174          141          422          202          186          690 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
         414          165          230          184           70           89 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
         382          100           77          129          214           61 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 TCGA-75-5122 
           3         1600          164          621          519           NA 
TCGA-75-5125 TCGA-75-5126 TCGA-75-5146 TCGA-75-5147 TCGA-75-6203 TCGA-75-6205 
          NA           NA           NA           NA           NA           NA 
TCGA-75-6206 TCGA-75-6207 TCGA-75-6211 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 
          NA           NA           NA           NA           NA           NA 
TCGA-75-7027 TCGA-75-7030 TCGA-75-7031 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
          NA           NA           NA           NA           NA           NA 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
          NA           NA         1093           NA         1202          760 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
          NA           NA           NA           NA         1221          678 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
         215           NA         6812           NA           NA           NA 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
          NA           NA           NA          327          881           NA 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
         994         6346           NA         2360           NA           NA 
TCGA-80-5607 TCGA-80-5608 TCGA-80-5611 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
          NA           NA           NA          824           NA           NA 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
          11          630          422           NA          591           NA 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
         508          745           10           NA           13           24 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 
         479          489          476          482           16           NA 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
          19           26           35           45           34           18 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF 
          15          455          405           10           30           NA 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
          14           39          323           NA           60          310 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
          79          417          372          842          224           35 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
         492          505          174           36           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
         297          127          186           34            2           NA 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
         568          377          477          476          830           84 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         121          553          605          964         1965         1932 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
        1332          775          181           NA           22          107 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
         182           NA           87          147           15          148 
TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
         115          197          271          392          427          459 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
          44          170          154          114          287          282 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W 
         238          578          435          116            6          266 
TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 
          NA          312          111          102          827         1175 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
          84           NA           NA           NA           NA           NA 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
          NA           NA           NA           NA           NA           NA 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
          NA           NA           NA          142           NA           NA 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
          NA         1490          121 
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=104,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=250,	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=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=15,	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=88,	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:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'BATCH.NUMBER':	nDistinctValues=23,	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] "COMPLETENESS.OF.RESECTION"             
[12] "RACE"                                  
[13] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 417 columns, 1 survival variables, and 13 non-survival variables.
                              D                 
            "D" "Time to Death"          "Year" 
AGE, nv=50, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=8, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "PATHOLOGY.T.STAGE"
[1] "num to class table"
vv1
  1   2   3   4 
131 232  36  15 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "PATHOLOGY.N.STAGE"
[1] "num to class table"
vv1
  0   1   2   3 
266  78  63   1 
PATHOLOGY.M.STAGE, nv=5, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=12, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=88, binary=FALSE, numeric=TRUE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
