[1] "libdir: /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/ClinicalAnalysisAllGenes_new/broadinstitute.org/cancer.genome.analysis/00333/58/"
[1] "terrence_modification_tag: TRUE"
[1] "op: "
[1] "dfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/LIHC-TP/9830281/LIHC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LIHC-TP/10006007/LIHC-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/LIHC-TP/10006007/LIHC-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=176, in expression file=212, common to both=162
Number of genes in original expression dataset=17827
[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] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 162 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
          NA          849           NA           NA           NA           NA 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
          NA           NA           NA           NA           NA           NA 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
          NA         1351          421            8          680          289 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BW-A5NQ TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 
         444          387           NA            2            5           NA 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 
          12           NA           NA           NA           NA            3 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
           2            3            4         2425           NA           NA 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
          NA         3437           NA           79           NA          662 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
          NA         2415         2017          602         2301          204 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
          NA           NA         1495          183          887           NA 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 
          NA           NA           NA           NA           NA           NA 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
          NA           NA           NA           NA           NA           NA 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
          NA           NA         1008          989         2232           NA 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
         428          445          433          561          458           NA 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
        1711           NA         2245         2849           NA           NA 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
          NA         2018          334           NA          230          334 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
          44          843         3071          408          386          482 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
         423          406            7            6            6            6 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S 
           6            6            6            6          570          608 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
         357          334           NA          303          363           NA 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
          NA          987           NA           NA          848           NA 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
          NA            4            1           10         1836           12 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y 
          37         1553         1636          860         1779           NA 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
         655          673          780          180          594          585 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
         447          364          302          243          133          236 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
         182           NA           NA           NA          122           NA 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
         360          407           15          291          155          433 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
         391          265           52           NA          498          135 
Variable 1:'AGE':	nDistinctValues=51,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=65,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=89,	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=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=6,	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=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=15,	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] "HISTOLOGICAL.TYPE"         "COMPLETENESS.OF.RESECTION"
 [9] "RACE"                      "ETHNICITY"                
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 162 columns, 1 survival variables, and 10 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=51, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=9, 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 
67 41 44  9 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
