[1] "terrence_modification_tag"
[1] TRUE
[1] "dfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/LGG-TP/8100485/LGG-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt"
[1] "cfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LGG-TP/8142957/LGG-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/LGG-TP/8142957/LGG-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=362, in expression file=463, common to both=359
Number of genes in original expression dataset=18339
[1] "ALL"
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "DCCUPLOADDATE"                         
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "RADIATIONTHERAPY"                      
[11] "KARNOFSKYPERFORMANCESCORE"             
[12] "HISTOLOGICALTYPE"                      
[13] "RADIATIONS.RADIATION.REGIMENINDICATION"
[14] "BATCHNUMBER"                           

Input Data has 14 rows and 359 columns.

[1] "Batch" "14"   
[1] "Last Follow UP"
TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5390 
         143           NA           NA          552          323         1966 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6186 
        1222            3           NA          303           NA           NA 
TCGA-CS-6188 TCGA-CS-6290 TCGA-CS-6665 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 
         725          546          378          258          230          244 
TCGA-CS-6669 TCGA-CS-6670 TCGA-DB-5270 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
         225          201         3733         2493         2289         1458 
TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 TCGA-DB-5281 
        2218         1419         1526         1354         1112         2381 
TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XC TCGA-DB-A4XD TCGA-DB-A4XE 
         915          313          387          840          822          573 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O TCGA-DB-A64P 
         559         2219          383          335          573          511 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W 
         182          489          469          846          448          415 
TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5141 TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
         332           NA          968          922          438          244 
TCGA-DH-A669 TCGA-DH-A66B TCGA-DH-A66D TCGA-DH-A66F TCGA-DU-5847 TCGA-DU-5849 
          NA          901          479          237          548          443 
TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 
         531           NA          407          257          207         5546 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 
         576          532          461         6423         1585          682 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 
        1491         2286         1401           NA           37         2660 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 
         214           NA           NA          605           NA           NA 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 
        3470          242          235           NA           NA         4752 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
        4206           NA           NA           NA           NA           NA 
TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-7294 
        2761           NA          800           NA           NA         2869 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7300 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 
          NA           NA           NA           NA         1834           NA 
TCGA-DU-7306 TCGA-DU-7309 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-8163 
        1277           84           NA           NA          121          629 
TCGA-DU-8164 TCGA-DU-8165 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP 
         651          582          516          471          431          433 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY 
         383          460          151          111          172          371 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76O 
         263           82          220          182           NA          217 
TCGA-DU-A76R TCGA-DU-A7T8 TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
          NA         3787         1525         2052         1251         2433 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-5322 TCGA-EZ-7264 
        1762         4084         2379         2907         3978          436 
TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6689 
        1453          547         1045          979          571          454 
TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-6692 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
         760          729          413          467          544         1219 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8185 
         686          627          611          394          416          433 
TCGA-FG-8186 TCGA-FG-8187 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
         487          611          455          361          472          744 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60K 
          18          160          113          294          214          202 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A710 
         214          128          124          322          328          698 
TCGA-FG-A713 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7470 
         159            4            3          203          238          268 
TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 
           4            1          503          114          530          199 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 
         738          194          216         2287         1800         1826 
TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 
        4690          122          153          908          705         3283 
TCGA-HT-7605 TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 
         139          526           NA          671         1399         1706 
TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 
        1752           NA          434            5          494           23 
TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 
        1359          184         1300            3          964          455 
TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7693 TCGA-HT-7694 TCGA-HT-7695 
           3            3           90          533          210          442 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 
        1201          585         1189            7         1540           15 
TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 TCGA-HT-7880 
         718         1130           10            4          112          162 
TCGA-HT-7881 TCGA-HT-7882 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8011 
          89           52          343          956           50          494 
TCGA-HT-8012 TCGA-HT-8013 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 
         286           NA          654         1004          372          190 
TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8110 TCGA-HT-8111 
           3           14           76          120          143            7 
TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8558 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DS 
         900          118           52          488          478            7 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R9 TCGA-HT-A5RA TCGA-HT-A5RB TCGA-HT-A5RC 
         319            4            2          447            3           NA 
TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A618 TCGA-HW-7486 
          82          396           55          491          162          910 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7490 TCGA-HW-7491 TCGA-HW-7493 TCGA-HW-7495 
         409          253          585         1222         1092          131 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KK 
         262          272          646          542          321          240 
TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-IK-8125 TCGA-P5-A5EW TCGA-P5-A5F0 
         294          201           NA         1301          204          125 
TCGA-P5-A5F1 TCGA-P5-A5F6 TCGA-QH-A65R TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65X 
         179           39          175           77          147          237 
TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY 
         125           NA           90           NA           NA           67 
TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 
          96           18          192          119          144           58 
TCGA-QH-A6XA TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-R8-A73M 
           7          153         2702         2860          993         1806 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TZ 
          NA         2101          571          860          856          658 
TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA 
         344          475          300         2878         2546           NA 
TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
        3156         2208         2146          697         2149          331 
TCGA-S9-A6WM TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
         283          231          187          103          434           NA 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
         383          128          249           62          247          109 
TCGA-S9-A7QX TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R8 
         123          554          396           NA         2649           NA 
TCGA-TM-A7C3 TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF 
        1504         1093          770          687         1472 
Variable 1:'AGE':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=68,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=275,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'BATCH.NUMBER':	nDistinctValues=24,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "KARNOFSKY.PERFORMANCE.SCORE"           
[4] "HISTOLOGICAL.TYPE"                     
[5] "RADIATIONS.RADIATION.REGIMENINDICATION"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 359 columns, 1 survival variables, and 5 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=58, binary=FALSE, numeric=TRUE
SYT6|148281 
      15586 
GENDER, nv=2, binary=FALSE, numeric=FALSE
XIST|7503 
    17492 
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
RPL3|6122 
    13702 
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
AK2|204 
    446 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
EXD3|54932 
      5340 
[1] "saved param, results, example.expr in analysis.result.Rdata "
