[1] "terrence_modification_tag"
[1] TRUE
[1] "dfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/miRseq_preprocessor/KICH-TP/6154420/0.miRseq_preprocessor.Finished/KICH-TP.miRseq_RPKM_log2.txt"
[1] "cfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KICH-TP/6154424/KICH-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/KICH-TP/6154424/KICH-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=70, in expression file=66, common to both=66
Number of genes in original expression dataset=469
[1] "ALL"
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                     "VITALSTATUS"                     
 [3] "DAYSTODEATH"                      "DAYSTOLASTFOLLOWUP"              
 [5] "PRIMARYSITEOFDESEASE"             "NEOPLASM.DISEASESTAGE"           
 [7] "PATHOLOGY.T.STAGE"                "PATHOLOGY.N.STAGE"               
 [9] "PATHOLOGY.M.STAGE"                "DCCUPLOADDATE"                   
[11] "GENDER"                           "DATEOFINITIALPATHOLOGICDIAGNOSIS"
[13] "RADIATIONTHERAPY"                 "KARNOFSKYPERFORMANCESCORE"       
[15] "HISTOLOGICALTYPE"                 "NUMBERPACKYEARSSMOKED"           
[17] "YEAROFTOBACCOSMOKINGONSET"        "GLEASON_SCORE"                   
[19] "PSA_VALUE"                        "DAYS_TO_PSA"                     
[21] "BATCHNUMBER"                     

Input Data has 21 rows and 66 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
          NA         4311           NA         3321         4169         3126 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
        2752         3304         3009         2582         2990         2949 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
        2815           NA         1364         2632           NA         2024 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
          NA         2248         1815          876         1664         1896 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
        4621          247          994          400         1082         1128 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
        3745         1552          953         3473          714         2674 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
         775          788         1983         2211          107           17 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8430 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
          NA         2063           NA          712           76          341 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
        1124         2727          636         2303         2339           NA 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 
        2279         2404         2820           NA         2445         2670 
TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
        3141         2618         2368         1739         1873         1944 
Variable 1:'AGE':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=57,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	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=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'NUMBERPACKYEARSSMOKED':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=8,	numeric=TRUE,	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=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                         "NEOPLASM.DISEASESTAGE"      
[3] "PATHOLOGY.T.STAGE"           "PATHOLOGY.N.STAGE"          
[5] "PATHOLOGY.M.STAGE"           "GENDER"                     
[7] "KARNOFSKY.PERFORMANCE.SCORE" "NUMBERPACKYEARSSMOKED"      
[9] "YEAROFTOBACCOSMOKINGONSET"  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 66 columns, 1 survival variables, and 9 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=39, binary=FALSE, numeric=TRUE
HSA-MIR-1180 
          24 
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
HSA-MIR-376A-1 
           290 
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
HSA-MIR-181B-1 
           110 
[1] "PATHOLOGY.T.STAGE"
[1] "num to class table"
vv1
 1  2  3  4 
21 25 18  2 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
HSA-MIR-92B 
        457 
[1] "PATHOLOGY.N.STAGE"
[1] "num to class table"
vv1
 0  1  2 
40  3  2 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
HSA-MIR-29B-1 
          189 
GENDER, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-219-1 
          165 
KARNOFSKY.PERFORMANCE.SCORE, nv=4, binary=FALSE, numeric=TRUE
HSA-MIR-7-1 
        432 
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "num to class table"
vv1
 70  80  90 100 
  1   2   5   3 
NUMBERPACKYEARSSMOKED, nv=10, binary=FALSE, numeric=TRUE
HSA-MIR-184 
        116 
YEAROFTOBACCOSMOKINGONSET, nv=8, binary=FALSE, numeric=TRUE
HSA-MIR-550A-2 
           383 
[1] "saved param, results, example.expr in analysis.result.Rdata "
