[1] "terrence_modification_tag"
[1] TRUE
[1] "dfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/CESC-TP/6154389/CESC-TP.meth.by_min_clin_corr.data.txt"
[1] "cfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/CESC-TP/6154388/CESC-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/CESC-TP/6154388/CESC-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=84, in expression file=179, common to both=84
Number of genes in original expression dataset=20141
[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] "HISTOLOGICALTYPE"                      
[14] "RADIATIONS.RADIATION.REGIMENINDICATION"
[15] "NUMBERPACKYEARSSMOKED"                 
[16] "NUMBER.OF.LYMPH.NODES"                 
[17] "GLEASON_SCORE"                         
[18] "PSA_VALUE"                             
[19] "DAYS_TO_PSA"                           
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 84 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN 
        1505          925           NA         1112         5385           NA 
TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY 
          NA         1616           NA           NA           NA         2382 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
        2669         1791           NA           81         2127         2892 
TCGA-DS-A1O9 TCGA-DS-A1OA TCGA-DS-A1OB TCGA-DS-A1OC TCGA-DS-A1OD TCGA-DS-A3LQ 
         266          879           NA          376         3096          183 
TCGA-DS-A5RQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
         208            8           53           40           25           19 
TCGA-EA-A3HU TCGA-EA-A3Y4 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
          81          440          441           54            9           10 
TCGA-EA-A50E TCGA-EA-A5ZD TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
           8           21           NA          619          241          211 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
         447          135          185           37           37           30 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
          66            2           31           44           48           45 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-HG-A2PA TCGA-HM-A3JJ 
          24          106           41           31          773           NA 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
         632          454         4482         3780           NA         3571 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-LP-A4AU 
        2948         2393         2493          808         1106            3 
TCGA-LP-A4AV TCGA-LP-A4AW TCGA-LP-A4AX TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD 
          NA           27            2          422            1          904 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
           2          132          113          103          112          174 
Variable 1:'AGE':	nDistinctValues=41,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=67,	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=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
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=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'HISTOLOGICAL.TYPE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBERPACKYEARSSMOKED':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'PSA_VALUE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 19:'DAYS_TO_PSA':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "PATHOLOGY.T.STAGE"                     
[3] "PATHOLOGY.N.STAGE"                     
[4] "PATHOLOGY.M.STAGE"                     
[5] "HISTOLOGICAL.TYPE"                     
[6] "RADIATIONS.RADIATION.REGIMENINDICATION"
[7] "NUMBERPACKYEARSSMOKED"                 
[8] "NUMBER.OF.LYMPH.NODES"                 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "2"          
[1] "PATHOLOGY.N" "3"          
Output Data has 84 columns, 1 survival variables, and 8 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=41, binary=FALSE, numeric=TRUE
DAPK2 
 4588 
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
ZBTB41 
 19388 
[1] "PATHOLOGY.T.STAGE"
[1] "num to class table"
vv1
 1  2  3  4 
53 22  1  2 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PRPF40A 
  13971 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
DUOX2 
 5187 
HISTOLOGICAL.TYPE, nv=5, binary=FALSE, numeric=FALSE
MAP4K4 
 10306 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
CTF1 
4375 
NUMBERPACKYEARSSMOKED, nv=11, binary=FALSE, numeric=TRUE
SMARCA4 
  16339 
NUMBER.OF.LYMPH.NODES, nv=7, binary=FALSE, numeric=TRUE
BAP1__1 
   1363 
[1] "saved param, results, example.expr in analysis.result.Rdata "
