[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_MethylationPreprocess/LUSC-TP/11494026/LUSC-TP.meth.by_min_clin_corr.data.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LUSC-TP/11541613/LUSC-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/LUSC-TP/11541613/LUSC-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=422, in expression file=359, common to both=288
Number of genes in original expression dataset=20228
[1] "ALL"
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [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] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "COMPLETENESS.OF.RESECTION"             
[21] "RACE"                                  
[22] "ETHNICITY"                             
[23] "BATCHNUMBER"                           

Input Data has 23 rows and 288 columns.

[1] "Batch" "23"   
[1] "Last Follow UP"
TCGA-18-3417 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-5782 TCGA-21-5783 
         758         2754           92          827          962           NA 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-4593 TCGA-22-4599 
        1268         1032          329          979         1067         1161 
TCGA-22-4601 TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
        1057           NA           NA          358          965         1975 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
        1933          445         1346           24         1651         2170 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
          NA          357          573          916         1912         1713 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
         506           29         5287         3149         4299          428 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-34-5231 TCGA-34-5232 
          NA           NA           NA          822         1528         2062 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
        1715           NA          707          365          428          941 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-37-5819 
         552           NA           NA          166           NA          103 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
        1454         2253         1361         2086           NA         2130 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
        1849           52          740           59          833         1107 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-5668 
         474         1084         1086          544           NA          349 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 
         849          376          757          310           NA           NA 
TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
         212          236         2023          407          358           NA 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 
         353          296          432          366          324          423 
TCGA-51-6867 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
          NA          541           NA          923           NA           NA 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 
           3          555           62           26           30           13 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
          30           44           40           26            6           NA 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 
           1           41          178           55           36           63 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
          17           16           34           38            2           46 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8386 
          30           25            4            4            8           NA 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 
          NA          378          911         2167           NA         1058 
TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2697 
        2589           NA         1723         1072          910           NA 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2709 TCGA-63-5128 TCGA-63-5131 TCGA-63-6202 
          NA           NA         1505           NA           NA           NA 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-68-7755 TCGA-68-7756 
          NA           NA           NA           NA           83          202 
TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 
         211          244           96          121          104           NA 
TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
          NA           NA           NA           NA           NA           NA 
TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
        2737           NA           15         1286           NA           NA 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 
          NA           NA          479           NA           NA         1641 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
          NA         2522           NA           NA           NA           NA 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8146 
        3166           NA           NA          833           NA         2183 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
         293           NA         1684         1092           10           NA 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
        4026         3576           NA           NA         1290         1280 
TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-79-5596 TCGA-85-6175 TCGA-85-6560 
          NA          839          713           NA           NA          364 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
         395           34           18           10           49            1 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
          NA           35          911           60           26           60 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
          16          960          428          513           13           11 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
          13           54           60           55           67           54 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
          61           61           22           21          445          424 
TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB 
          NA            3          475           15           NA           NA 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
          NA           NA           NA           25           19           NA 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
          NA           NA           NA           24           13          111 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED 
         758          289           89          358          428          244 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
         331          269           82          106          122          160 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 
          70           87           NA          356          430         1213 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 
        1344          189          211          273          183          256 
TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 
          NA          413          224          308          222           35 
TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
         449           36           83         1722         1548         1135 
Variable 1:'AGE':	nDistinctValues=43,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=88,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=181,	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=8,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=80,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'BATCH.NUMBER':	nDistinctValues=24,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "KARNOFSKY.PERFORMANCE.SCORE"           
 [8] "HISTOLOGICAL.TYPE"                     
 [9] "RADIATIONS.RADIATION.REGIMENINDICATION"
[10] "NUMBERPACKYEARSSMOKED"                 
[11] "COMPLETENESS.OF.RESECTION"             
[12] "RACE"                                  
[13] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 288 columns, 1 survival variables, and 13 non-survival variables.
                              D                 
            "D" "Time to Death"          "Year" 
AGE, nv=43, 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 
 76 166  37   9 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "PATHOLOGY.N.STAGE"
[1] "num to class table"
vv1
  0   1   2 
179  79  24 
PATHOLOGY.M.STAGE, nv=4, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=80, binary=FALSE, numeric=TRUE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
