[1] "terrence_modification_tag"
[1] TRUE
[1] "dfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/UCEC-TP/6458233/UCEC-TP.meth.by_min_clin_corr.data.txt"
[1] "cfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/UCEC-TP/6154844/UCEC-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/UCEC-TP/6154844/UCEC-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=481, in expression file=406, common to both=364
Number of genes in original expression dataset=20424
[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] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "GLEASON_SCORE"                         
[19] "PSA_VALUE"                             
[20] "DAYS_TO_PSA"                           
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 364 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-A5-A0G1 TCGA-A5-A0GG TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0VO TCGA-A5-A1OF 
          NA         2656         1167         1120          364          241 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 
         348         1104          292          243         2768         1409 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M 
          NA          161          156          223          455           31 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
          33           60           12          602           31           61 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BH TCGA-AJ-A3BI 
          91           15           34           31           NA           61 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
          51           NA           64           65           50           39 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH 
          28          210           78           41           52           23 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A059 
          59          142           57           56           51          250 
TCGA-AP-A05O TCGA-AP-A0LF TCGA-AP-A0LM TCGA-AP-A0LS TCGA-AP-A1DH TCGA-AP-A1DK 
         371          103          825         1918         2180         1836 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
        1700          952           NA         1275         1495          204 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
         940          317          847          494          555         1026 
TCGA-AW-A1PO TCGA-AX-A06D TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ 
          17           NA          833         1844         1065         1333 
TCGA-AX-A0J0 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
        1219          404          584          515          412          464 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
         617          378          610         2337         2207         1645 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 
        2052          764         1107          337           NA           NA 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
        2167         1020         1861         2090         1016         1232 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
         489          660          539          831           NA           NA 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
        1176            7            3           10            4            6 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
          NA            1            4           NA            7           36 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JX 
         254          440            4         1312         1483         1360 
TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
         542          124          265         5650         3447         2687 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
        2303         1656         1396         1361         1337         1245 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
        1120          975         1019          831          509          594 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
         592          595          559          528          504         5835 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
          NA           NA          438          447          355           NA 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-BG-A0MA TCGA-BG-A0MH 
         465          389         1890          152           NA         1341 
TCGA-BG-A0MK TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
          NA          224          260          131          490          868 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
         907         1151          451          382          419          448 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
         426          470          470          434           55          291 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CA 
          NA           16          177          344          207         1064 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD 
         311          309          966          760          734          211 
TCGA-BK-A56F TCGA-BS-A0T9 TCGA-BS-A0U5 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UL 
         200           NA         2935         2044         2686         2481 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
        1810         1910         1934         1507         1921         2021 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
         512          602          911          260           17          147 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
         872          728          685           53          135          669 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
        1201          915          909           NA          112          892 
TCGA-D1-A162 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
        1145          991           20          478         1098         1135 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
        1106         1141         1119           80           NA           NA 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
         909          945         1022          324           21          568 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
          43          111          532          594          202          917 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
         548          206           48          212           30          926 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
          39          852          854          802          311           46 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
          54           NA          739           70          697           43 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
         402           22          555          513          548           63 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
         458           32           NA          107         1260           NA 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU 
        1365            8          130          125          495         1195 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU 
        1114          739         1076           NA           NA           NA 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
        2797          711         1471          518           NA          202 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
         487          223          510          332          243          328 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
         972         1066         1004          825          981          761 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EY-A1G7 
         974           NA         1046          589          392           NA 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
          NA          138          248          741          826          709 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
         709          727          693          424          209          586 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
         573          544          536          459          490          378 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 
         481          260          197          588          383          109 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
         438          574          694          409         1392          943 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 
         884          832          421          196          544           65 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
         212          113          160         1217         1064         1034 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
        1095           NA           NA          273         2953         1795 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
         276           NA          880          761          791           NA 
TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC 
          53          203           73          329 
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=40,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=293,	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=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 19:'PSA_VALUE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'DAYS_TO_PSA':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=22,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "HISTOLOGICAL.TYPE"                     
[3] "RADIATIONS.RADIATION.REGIMENINDICATION"
[4] "COMPLETENESS.OF.RESECTION"             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 364 columns, 1 survival variables, and 4 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=58, binary=FALSE, numeric=TRUE
ANGPT4 
   646 
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
APBB1IP 
    822 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
MAP2K2 
 10434 
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
TNFRSF19 
   18317 
[1] "saved param, results, example.expr in analysis.result.Rdata "
