
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/BRCA-TP/2904311/0.GDAC_MethylationPreprocess.Finished/BRCA-TP.meth.for_correlation.filtered_data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/BRCA-TP/2843115/1.GDAC_clinicalDataPicker.Finished/BRCA-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=875, in expression file=536, common to both=529
Number of genes in original expression dataset=17321
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "RADIATIONTHERAPY"                      
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "DISTANT.METASTASIS"                    
[13] "LYMPH.NODE.METASTASIS"                 
[14] "NUMBER.OF.LYMPH.NODES"                 
[15] "TUMOR.STAGECODE"                       
[16] "NEOPLASM.DISEASESTAGE"                 
[17] "BATCHNUMBER"                           

Input Data has 17 rows and 529 columns.

[1] "Batch" "17"   
[1] "Last Follow UP"
TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK 
        1463          433         1437          634          426           NA 
TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04R 
         242         1196          852          583          553         2364 
TCGA-A2-A0CT TCGA-A2-A0EN TCGA-A2-A0EU TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
        1917         2515          733         1643         1351           NA 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
          NA         1288         1154          337          322           NA 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD 
         395          321          344          397          643          550 
TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ 
         252          289          404          379          358          326 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW 
         334          268          661           NA          460          221 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
         935          409          380          371          372          132 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
        1285         2968          258          285          243         2511 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A7-A0D9 TCGA-A7-A13D TCGA-A7-A13E 
         113          363          803          159          267          287 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
         196          208          421          257          209           64 
TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
         122           67          181          151          148           76 
TCGA-A7-A3J1 TCGA-A8-A075 TCGA-A8-A08O TCGA-A8-A0A6 TCGA-A8-A0AD TCGA-AC-A23C 
          75          517          942          640         1157           29 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM 
          72          329           81           44         1172         1162 
TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH 
          44         1685         1125         1180         1542           31 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
          21           35           10           10          375            9 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
          10           10           10           10          162          170 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03U TCGA-AO-A0JA TCGA-AO-A0JC 
        2442         1455         1645           NA          346         1547 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
        1813         1965          354          449         1172         1512 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
        1319         1826         3119         3018         2850         2877 
TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12C TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A1KO 
        2923         2359         1993         1742         1265          448 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H 
        2513         1519         2140           16          541          439 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ 
        3344           NA          230          162         2392         1500 
TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TU TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
          NA         1679          360          904          739           15 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AI 
        1313            8           NA         2263         1627         1881 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
        1604         1558         1485         1329         1324         1215 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
        1309           NA         1242         1409         1295         1072 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
        1103          614         3333         1548         2221         1990 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
        2074         1997           26         2008         1745         1888 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
        1620         1623         1648         1550         1465         1574 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
        1707         1373         1236         1212         1058           NA 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
        3913           NA         1303          223         1217          519 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-B6-A0I1 TCGA-B6-A0IK TCGA-B6-A0RE 
         633          516          620           NA           NA         6434 
TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
        2082         6795           NA           NA         5261         4928 
TCGA-B6-A0RP TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WT 
          NA           NA         2721         3991         4788         5396 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X1 
          NA          546           NA           NA         3941         5671 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI 
          NA           NA           NA         1326         3088         1463 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B3 
        3330         4840          746          622          867         1203 
TCGA-BH-A0B5 TCGA-BH-A0B8 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BJ 
        1471         1569         1132          974          781          660 
TCGA-BH-A0BM TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 
        1117         1640         1386         1492         1270         1464 
TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DP 
        1393          713         1156          673          423          476 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DV TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
          98           77         1374          133          477          376 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H6 TCGA-BH-A0H7 
         917          328          461         1149          747          701 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HF TCGA-BH-A0HI TCGA-BH-A0HK 
        1247          856          806          727          619          178 
TCGA-BH-A0HP TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
         414          829          867          170          180          175 
TCGA-BH-A0W5 TCGA-BH-A0WA TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
         543          372           NA           NA           NA           NA 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 
          NA           NA           NA           NA          209           22 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28Q TCGA-C8-A1HE 
          NA           NA           NA           NA          196           NA 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL 
          NA           NA            2            5            7            2 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
           6            2           NA            9            7           11 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
          13            4            6            1            1            1 
TCGA-C8-A27A TCGA-C8-A27B TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
         371           30          256          248           18           NA 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH 
         178          273           57           96          187          284 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
          21          274          109          265          238          217 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
         167          105          123          106          171          236 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
          85          272          380          274          201           81 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
         155          197          196          352          326          319 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
         218          242          177          168           50          193 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
         149          146          117           81          120          166 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
         115           72          124          182          227          209 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
         140          185          118          125          144          145 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-E2-A105 
          23           90          135           73           15         1163 
TCGA-E2-A106 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
        1555          124         1172          748          853          418 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A1AZ 
         360         1350          411          463           34         1964 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1BC TCGA-E2-A1BD 
        1271         1361          911          774          297          317 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
         983          956          755          658          850          725 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
         518           14          392          448          127         1312 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG 
         633         1015          388          463          972          350 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A1LS TCGA-E2-A3DX 
        2875         2750           NA         1014          239          217 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
          NA           NA           NA           NA           NA           NA 
TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH 
          NA           NA           NA           NA           NA           NA 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
          NA           NA           NA           19           64           29 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
          42           84           34           21         1228           20 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
          47           38           14           48           16           24 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E 
          NA           NA           NA           NA           NA           NA 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 
          NA           NA           43           20           25           12 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
          21           28           10           21           13           23 
TCGA-E9-A3HO TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1J1 TCGA-EW-A1J2 
          19          252         1082          258          282          139 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
         252          227          595          522          463          562 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 
         593          941         1121          987          501          365 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC 
         312          635           NA          267          608          186 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR 
         174          106          139          875          139         1120 
TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 
        1173          238          190          212          703           NA 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH 
        5909         1615         1628         1309         1299         1286 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
        1883         1896         2762         2331         2352         1622 
TCGA-GM-A3NY 
         743 
Variable 1:'AGE':	nDistinctValues=62,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=380,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TUMOR.STAGECODE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NEOPLASM.DISEASESTAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'BATCH.NUMBER':	nDistinctValues=20,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "RADIATIONS.RADIATION.REGIMENINDICATION"
[4] "DISTANT.METASTASIS"                    
[5] "LYMPH.NODE.METASTASIS"                 
[6] "NUMBER.OF.LYMPH.NODES"                 
[7] "TUMOR.STAGECODE"                       
[8] "NEOPLASM.DISEASESTAGE"                 
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
 T1 T1A T1B T1C  T2  T3  T4 T4B T4D  TX 
 28   1   5 107 310  59   3  13   1   2 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 529 columns, 1 survival variables, and 8 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
CDC73 
 3047 
AGE, nv=62, binary=FALSE, numeric=TRUE
KIF15 
 7908 
GENDER, nv=2, binary=FALSE, numeric=FALSE
ALDOC 
  478 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
CCDC86 
  2830 
DISTANT.METASTASIS, nv=4, binary=FALSE, numeric=FALSE
NHEDC1 
 10265 
LYMPH.NODE.METASTASIS, nv=15, binary=FALSE, numeric=FALSE
SS18L1 
 14448 
NUMBER.OF.LYMPH.NODES, nv=25, binary=FALSE, numeric=TRUE
TCP11L1 
  14916 
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
[1] "Clinical variable TUMOR.STAGECODE has too few non-missing values, n=0"
NEOPLASM.DISEASESTAGE, nv=12, binary=FALSE, numeric=FALSE
IDH3B 
 7191 
> q(save="no")
