[1] "terrence_modification_tag"
[1] TRUE
[1] "dfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_RPPA_preprocess/PRAD-TP/5956391/PRAD-TP.rppa.txt"
[1] "cfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PRAD-TP/6154773/PRAD-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/PRAD-TP/6154773/PRAD-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=186, in expression file=164, common to both=143
Number of genes in original expression dataset=189
[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] "RADIATIONTHERAPY"                      
[14] "HISTOLOGICALTYPE"                      
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "COMPLETENESS.OF.RESECTION"             
[17] "NUMBER.OF.LYMPH.NODES"                 
[18] "GLEASON_SCORE_COMBINED"                
[19] "GLEASON_SCORE_PRIMARY"                 
[20] "GLEASON_SCORE_SECONDARY"               
[21] "HIGHEST_GLEASON_SCORE"                 
[22] "GLEASON_SCORE"                         
[23] "PSA_RESULT_PREOP"                      
[24] "DAYS_TO_PREOP_PSA"                     
[25] "PSA_VALUE"                             
[26] "DAYS_TO_PSA"                           
[27] "BATCHNUMBER"                           

Input Data has 27 rows and 143 columns.

[1] "Batch" "27"   
[1] "Last Follow UP"
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
          91          212          671           31          395          424 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
          60           91           31          395         1065          942 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
          31           62           28         1339          365           31 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
         700           31          458          731           62          395 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
         485          820          303          974         1004           91 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
         881          825         1006          594          396          905 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
         532          936          244          716          880          921 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
         827          727         1184         1096         1115          974 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
        1172         1102         1240         1416         1454         1590 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
        1335         1578         1462         1310         1115         1179 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
        1209         1272          920         1461          884          821 
TCGA-EJ-7125 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7321 TCGA-EJ-7328 
        1860          295          289          285          233          170 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
         191            9          169           64          131          167 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
         258          442           52          552          596          526 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
          43          700          369         1946          821          314 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-FC-7708 TCGA-FC-7961 
         162          128          519          299           32           70 
TCGA-FC-A5OB TCGA-G9-6329 TCGA-G9-6338 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6351 
         273         1266         2028         1696          554         1403 
TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
        1541         1434         1415         1443         1378         1198 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        1363          101         1222         1156         1226          811 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6499 
         958         1155          765         1771         1726         1543 
TCGA-G9-7510 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 
        1185          486          648          856          512          184 
TCGA-HC-7077 TCGA-HC-7079 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7233 
          NA           89           30          881           60           52 
TCGA-HC-7736 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7748 TCGA-HC-7817 TCGA-HI-7168 
          30           53           51          792           32         2391 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
        1949         1899           NA           98          374 
Variable 1:'AGE':	nDistinctValues=29,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=TRUE.
Variable 3:'DAYSTODEATH':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=124,	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=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
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=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'COMPLETENESS.OF.RESECTION':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'GLEASON_SCORE_COMBINED':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'GLEASON_SCORE_PRIMARY':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'GLEASON_SCORE_SECONDARY':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 21:'HIGHEST_GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'GLEASON_SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 23:'PSA_RESULT_PREOP':	nDistinctValues=98,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 24:'DAYS_TO_PREOP_PSA':	nDistinctValues=68,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 25:'PSA_VALUE':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 26:'DAYS_TO_PSA':	nDistinctValues=124,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 27:'BATCH.NUMBER':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                       "PATHOLOGY.T.STAGE"        
 [3] "PATHOLOGY.N.STAGE"         "COMPLETENESS.OF.RESECTION"
 [5] "NUMBER.OF.LYMPH.NODES"     "GLEASON_SCORE_COMBINED"   
 [7] "GLEASON_SCORE_PRIMARY"     "GLEASON_SCORE_SECONDARY"  
 [9] "GLEASON_SCORE"             "PSA_RESULT_PREOP"         
[11] "DAYS_TO_PREOP_PSA"         "PSA_VALUE"                
[13] "DAYS_TO_PSA"              
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "2"          
[1] "PATHOLOGY.N" "3"          
Output Data has 143 columns, 1 survival variables, and 13 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
[1] "Survival variable Time to Death has too few event occurrence, nEvent=1"
AGE, nv=29, binary=FALSE, numeric=TRUE
EIF4EBP1|4E-BP1_PT37_T46-R-V 
                           6 
PATHOLOGY.T.STAGE, nv=3, binary=FALSE, numeric=TRUE
EIF4G1|EIF4G-R-C 
             175 
[1] "PATHOLOGY.T.STAGE"
[1] "num to class table"
vv1
 2  3  4 
55 82  5 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PEA15|PEA15_PS116-R-V 
                  111 
COMPLETENESS.OF.RESECTION, nv=3, binary=FALSE, numeric=FALSE
MAPK1 MAPK3|MAPK_PT202_Y204-R-V 
                             91 
NUMBER.OF.LYMPH.NODES, nv=7, binary=FALSE, numeric=TRUE
CDKN1B|P27_PT157-R-C 
                 180 
GLEASON_SCORE_COMBINED, nv=5, binary=FALSE, numeric=TRUE
BCL2L11|BIM-R-V 
             35 
[1] "GLEASON_SCORE_COMBINED"
[1] "num to class table"
vv1
  6   7   8   9  10 
  9 102  12  18   2 
GLEASON_SCORE_PRIMARY, nv=4, binary=FALSE, numeric=TRUE
ESR1|ER-ALPHA_PS118-R-V 
                     62 
[1] "GLEASON_SCORE_PRIMARY"
[1] "num to class table"
vv1
 2  3  4  5 
 1 73 64  5 
GLEASON_SCORE_SECONDARY, nv=3, binary=FALSE, numeric=TRUE
BCL2L11|BIM-R-V 
             35 
[1] "GLEASON_SCORE_SECONDARY"
[1] "num to class table"
vv1
 3  4  5 
46 79 18 
GLEASON_SCORE, nv=5, binary=FALSE, numeric=TRUE
BCL2L11|BIM-R-V 
             35 
[1] "GLEASON_SCORE"
[1] "num to class table"
vv1
 6  7  8  9 10 
 9 97 14 21  2 
PSA_RESULT_PREOP, nv=98, binary=FALSE, numeric=TRUE
EEF2|EEF2-R-C 
          172 
DAYS_TO_PREOP_PSA, nv=68, binary=FALSE, numeric=TRUE
EGFR|EGFR_PY1173-R-V 
                  60 
PSA_VALUE, nv=44, binary=FALSE, numeric=TRUE
PEA15|PEA15-R-V 
            110 
DAYS_TO_PSA, nv=124, binary=FALSE, numeric=TRUE
EEF2K|EEF2K-R-V 
            173 
[1] "saved param, results, example.expr in analysis.result.Rdata "
