[1] "terrence_modification_tag"
[1] TRUE
[1] "dfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/LUAD-TP/6044650/LUAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt"
[1] "cfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LUAD-TP/6154697/LUAD-TP.merged_data.txt"
[1] "gv"
[1] "ALL"
[1] "gfn"
[1] "ALL"
[1] "sfn"
[1] ""
[1] "fv"
[1] "ALL"
[1] "ofn"
[1] ""
[1] "dx"
[1] ""
[1] "sfn"
[1] ""
[1] FALSE
[1] "cfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LUAD-TP/6154697/LUAD-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=461, in expression file=488, common to both=450
Number of genes in original expression dataset=18308
[1] "ALL"
[1] "terrence_modification_tag"
[1] TRUE
[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] "GLEASON_SCORE"                         
[22] "PSA_VALUE"                             
[23] "DAYS_TO_PSA"                           
[24] "BATCHNUMBER"                           

Input Data has 24 rows and 450 columns.

[1] "Batch" "24"   
[1] "Last Follow UP"
TCGA-05-4244 TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 
          NA         1523           NA          606          426         1369 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 
        1126           NA           NA           NA         1431           NA 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 
         578          610           NA           NA          454           NA 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
         911          365          913          669          791          791 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
         761          761          730           NA          457          151 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
         881          670           30           62           14          224 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
         181          264         2973         3674         1147         1491 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
         863         1073          354         1357          448           NA 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
         133         1323         1429          400         1367          741 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
        1280         1301           97          246         1130         1163 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
        1036          189          722         1013          863          383 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         328          302          845          362          658          705 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
        1938           NA         1110           NA          444          325 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
         366          218          557           NA          882          535 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
         719          385           98          260          485          466 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
         287          135          114           76         2318           NA 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
          NA           NA         1081         1421          428          999 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
         268          896          157         1700          457          369 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
         890          521          354           NA           NA         2174 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
        2146          455          785          944         1499          245 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
         282          267         1091         2369          653           NA 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
          NA          567          882          764          686           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-53-A4EZ 
          NA          255           NA           NA          424          280 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
         701         1178         1479         1374           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-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
          40           NA           39           31           31           24 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
          54           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-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
          11           NA           NA          227            9            3 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
         146          212           15           48           49           65 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
         105           33           29           NA            1           28 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
           5           47          161           NA         1215         1289 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
          NA         2345         1444           NA           NA           NA 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
          NA         2067         2199           NA         1245          910 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
        1728          628         1189         1685         1126           NA 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
        2676           62         1305          864         1559          865 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 
          30          609          573          427          385           NA 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
         173          140          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           99           76          128          214           61 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        1599          711          911          799          467          130 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-5122 
          40          164           38          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         1201          760 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
          NA           NA           NA           NA         1220          678 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
         214           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         6345           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          823           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          332          476          482           16           NA 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
          19           26           34           44           33           17 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF 
          15          454          404           10           30           NA 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
          13           39          323           NA           60          309 
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          196          173           36           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 
         297          127          185           34            2          163 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 
          21           40          132          123          963         1965 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
        1932         1331          775          181           NA           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
         106          181           NA           86          146           15 
TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
         197          271          392          427          458           44 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
         169          153          113          287          282          238 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
         212           76          116            6          285          621 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T6 
         353           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-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 
          NA          142           NA           NA           NA         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=111,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=268,	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=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=39,	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=89,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'PSA_VALUE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 23:'DAYS_TO_PSA':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 24:'BATCH.NUMBER':	nDistinctValues=30,	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 450 columns, 1 survival variables, and 12 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=50, binary=FALSE, numeric=TRUE
AHRR|57491 
       421 
NEOPLASM.DISEASESTAGE, nv=8, binary=FALSE, numeric=FALSE
ZNF540|163255 
        18018 
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
C14ORF139|79686 
           1757 
[1] "PATHOLOGY.T.STAGE"
[1] "num to class table"
vv1
  1   2   3   4 
139 251  40  18 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
RCOR3|55758 
      13241 
[1] "PATHOLOGY.N.STAGE"
[1] "num to class table"
vv1
  0   1   2   3 
285  85  68   2 
PATHOLOGY.M.STAGE, nv=5, binary=FALSE, numeric=FALSE
CUL4A|8451 
      4139 
GENDER, nv=2, binary=FALSE, numeric=FALSE
PRKY|5616 
    12603 
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
SLC24A6|80024 
        14541 
HISTOLOGICAL.TYPE, nv=12, binary=FALSE, numeric=FALSE
A4GNT|51146 
         26 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
PGAM2|5224 
     11864 
NUMBERPACKYEARSSMOKED, nv=89, binary=FALSE, numeric=TRUE
C5ORF33|133686 
          2376 
YEAROFTOBACCOSMOKINGONSET, nv=57, binary=FALSE, numeric=TRUE
ANKRD33|341405 
           662 
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
PAX2|5076 
    11568 
[1] "saved param, results, example.expr in analysis.result.Rdata "
