[1] "libdir: /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/ClinicalAnalysisAllGenes_new/broadinstitute.org/cancer.genome.analysis/00333/60/"
[1] "terrence_modification_tag: TRUE"
[1] "op: "
[1] "dfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_RPPA_preprocess/ACC-TP/11487211/ACC-TP.rppa.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ACC-TP/11541222/ACC-TP.merged_data.txt"
[1] "gv: ALL"
[1] "gfn: "
[1] "sfn: "
[1] "fv: ALL"
[1] "ofn: "
[1] "dx: "
[1] "cfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ACC-TP/11541222/ACC-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=92, in expression file=46, common to both=46
Number of genes in original expression dataset=193
[1] "ALL"
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "NEOPLASM.DISEASESTAGE"                 
 [6] "PATHOLOGY.T.STAGE"                     
 [7] "PATHOLOGY.N.STAGE"                     
 [8] "PATHOLOGY.M.STAGE"                     
 [9] "DCCUPLOADDATE"                         
[10] "GENDER"                                
[11] "RADIATIONTHERAPY"                      
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCHNUMBER"                           

Input Data has 15 rows and 46 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 
          NA         2091         2703           NA           NA         1352 
TCGA-OR-A5JA TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JV 
          NA          149         3688          383          907         2023 
TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K3 
        2202           NA          211         1029         2938         3047 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KU 
         699          253         1493          749         1414         4673 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5LD TCGA-OR-A5LG 
        1525         1364           NA           NA           NA         1589 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN 
          NA           NA         2222           NA         1858         1916 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG 
        2102         1857         1096          549          709           NA 
TCGA-PA-A5YG TCGA-PK-A5H8 TCGA-PK-A5H9 TCGA-PK-A5HA 
         470         3240          616         1201 
Variable 1:'AGE':	nDistinctValues=36,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH.NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
[4] "PATHOLOGY.N.STAGE"     "GENDER"                "ETHNICITY"            
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 46 columns, 1 survival variables, and 6 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=36, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "PATHOLOGY.T.STAGE"
[1] "num to class table"
vv1
 1  2  3  4 
 2 29  7  7 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
