
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.13.3873/ClinicalAnalysisAllGenes.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ClinicalAnalysisAllGenes_new.13.3873/", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/THCA-TP/2602226/0.mRNAseq_preprocessor.Finished/THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/THCA-TP/2589062/1.GDAC_clinicalDataPicker.Finished/THCA-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=290, in expression file=409, common to both=271
Number of genes in original expression dataset=18025
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "RADIATIONTHERAPY"                      
[10] "HISTOLOGICALTYPE"                      
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "RADIATIONEXPOSURE"                     
[13] "DISTANT.METASTASIS"                    
[14] "EXTRATHYROIDAL.EXTENSION"              
[15] "LYMPH.NODE.METASTASIS"                 
[16] "COMPLETENESS.OF.RESECTION"             
[17] "NUMBER.OF.LYMPH.NODES"                 
[18] "TUMOR.STAGECODE"                       
[19] "NEOPLASM.DISEASESTAGE"                 
[20] "MULTIFOCALITY"                         
[21] "TUMOR.SIZE"                            
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 271 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
         479          356          232          182          197          251 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZF TCGA-BJ-A0ZG 
         264          122          183          237          210          230 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A192 TCGA-BJ-A28R 
          22          152           85           13          246          148 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28X TCGA-BJ-A290 TCGA-BJ-A3PR TCGA-BJ-A3PT 
          84          155          532          626          244          367 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-DE-A0XZ TCGA-DE-A0Y2 
          16            3            6            7          402          231 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
         952          161          286          274          215         4199 
TCGA-DJ-A13R TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
          92          758          393          362          454          243 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
         334         3041          549          212          243          151 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
         212           30          273           31          181          304 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT 
         242          152          623          318           59          292 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
         312          242          234          153          267          256 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
         247          284          206          280          287          301 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
         262          291          315          378          330          304 
TCGA-DJ-A3UN TCGA-DJ-A3US TCGA-DJ-A3UY TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
         380          630          405          225          540          443 
TCGA-DJ-A3V6 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VD 
         454          299          259          217          363          350 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VM TCGA-DO-A1JZ 
         134          235          253          528          481         1225 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
          93           70          945          365         1544         1222 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ 
        1421          635          427           34           11           NA 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
          45           10            7            5           22            8 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
          45           NA           16            5            7           35 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EM-A1CS TCGA-EM-A1CT 
         234          210           12           12          580          153 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
         214           NA          245          217          284         1421 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
        1209          650           81          207          202          138 
TCGA-EM-A22N TCGA-EM-A22P TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CM TCGA-EM-A2CN 
         209          174          249          209          357          344 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2OV 
         183           90          199          284          319          353 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
         219           88          347          284          191          194 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AN TCGA-EM-A3AO 
         224           10          397          282          341          336 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3O8 TCGA-EM-A3OB TCGA-ET-A25G 
         161          262          207           15           71         1088 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
          10          903          589          450          375           75 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
         135           15          621         1643          579          373 
TCGA-ET-A2N0 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
        1049          198           43         1182            9          362 
TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
          59         2535         1309          406         1413           20 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
         237           51          177          127           74          168 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
         752           39           72          137         2095         1536 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
        1366           65            9         3424          751           98 
TCGA-ET-A40S TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A233 TCGA-FE-A234 
         152         1565         1442          374          751         1333 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
        2031         2292         1215           NA         1907         2872 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SE TCGA-FK-A3SG 
        2589         1868         1913         1401          669           28 
TCGA-FK-A3SH TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
        1463           38           35           34           50           30 
TCGA-FY-A3NN TCGA-FY-A3NP TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
          NA           18           46           23            1          141 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
          66          278           NA           23           29          208 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-GE-A2C6 TCGA-H2-A26U 
         126          199          138           27          206          106 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
         145          148           90           67           88         1070 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
         939           80           99           68          392          415 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
          41          968          846          751          678          174 
TCGA-J8-A42S 
          75 
Variable 1:'AGE':	nDistinctValues=67,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=218,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=TRUE.
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=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RADIATIONEXPOSURE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'DISTANT.METASTASIS':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'EXTRATHYROIDAL.EXTENSION':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'LYMPH.NODE.METASTASIS':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'TUMOR.STAGECODE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NEOPLASM.DISEASESTAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'MULTIFOCALITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'TUMOR.SIZE':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=20,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "GENDER"                                
 [3] "HISTOLOGICAL.TYPE"                     
 [4] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [5] "RADIATIONEXPOSURE"                     
 [6] "DISTANT.METASTASIS"                    
 [7] "EXTRATHYROIDAL.EXTENSION"              
 [8] "LYMPH.NODE.METASTASIS"                 
 [9] "COMPLETENESS.OF.RESECTION"             
[10] "NUMBER.OF.LYMPH.NODES"                 
[11] "TUMOR.STAGECODE"                       
[12] "NEOPLASM.DISEASESTAGE"                 
[13] "MULTIFOCALITY"                         
[14] "TUMOR.SIZE"                            
[1] "TUMOR.?STAGE" "11"          
[1] "stage2"
vv
 T1 T1A T1B  T2  T3  T4 T4A  TX 
 23   9  52  93  86   1   6   1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 271 columns, 1 survival variables, and 14 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
[1] "Survival variable Time to Death has too few event occurrence, nEvent=1"
AGE, nv=67, binary=FALSE, numeric=TRUE
C12ORF52|84934 
          1679 
GENDER, nv=2, binary=FALSE, numeric=FALSE
DDX3Y|8653 
      4357 
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
FN1|2335 
    5992 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
FLJ37543|285668 
           5938 
RADIATIONEXPOSURE, nv=2, binary=FALSE, numeric=FALSE
FAM138F|641702 
          5425 
DISTANT.METASTASIS, nv=3, binary=FALSE, numeric=FALSE
ARRB1|408 
      974 
EXTRATHYROIDAL.EXTENSION, nv=3, binary=FALSE, numeric=FALSE
THNSL2|55258 
       15641 
LYMPH.NODE.METASTASIS, nv=5, binary=FALSE, numeric=FALSE
KCNN4|3783 
      8011 
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
CATSPER2P1|440278 
             2751 
NUMBER.OF.LYMPH.NODES, nv=26, binary=FALSE, numeric=TRUE
FAM60A|58516 
        5590 
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
[1] "Clinical variable TUMOR.STAGECODE has too few non-missing values, n=0"
NEOPLASM.DISEASESTAGE, nv=5, binary=FALSE, numeric=FALSE
CYP26A1|1592 
        4164 
MULTIFOCALITY, nv=2, binary=FALSE, numeric=FALSE
INMT|11185 
      7688 
TUMOR.SIZE, nv=55, binary=FALSE, numeric=TRUE
LRRC55|219527 
         9240 
> q(save="no")
