
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ClinicalAnalysisAllGenes_new.13.3873/ClinicalAnalysisAllGenes.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ClinicalAnalysisAllGenes_new.13.3873/", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/HNSC-TP/3026019/HNSC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/HNSC-TP/3132649/1.GDAC_clinicalDataPicker.Finished/HNSC-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=327, in expression file=303, common to both=302
Number of genes in original expression dataset=18388
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "HISTOLOGICALTYPE"                      
[11] "PATHOLOGICSPREAD(PT)"                  
[12] "PATHOLOGICSPREAD(PN)"                  
[13] "PATHOLOGICSPREAD(M)"                   
[14] "TUMORSTAGE"                            
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "NUMBERPACKYEARSSMOKED"                 
[17] "TOBACCOSMOKINGHISTORYINDICATOR"        
[18] "YEAROFTOBACCOSMOKINGONSET"             
[19] "NUMBER.OF.LYMPH.NODES"                 
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 302 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         461          283          415         1134          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         190          845         1761          186          179          242 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
        1635         1747          152          244           NA           63 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
          NA          113          236          186         2891          275 
TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
         140          557          310          535          422          718 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-CN-4722 TCGA-CN-4723 
         638         1152          427          436          192          412 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
         310          142          194          325          166          343 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
         383          522          226          369          395          240 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
         436          348          810          875          397          279 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 
         289          173          377          866          193          252 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
         493          351          360          352          380           NA 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
         413          274          207          228          143          154 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
         201          159           45          134           97          276 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
         201          188          224           42          177           83 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6997 TCGA-CN-6998 TCGA-CQ-5323 TCGA-CQ-5324 
         119           NA          100           46         1465         1207 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
         654           NA          841          896         1028          317 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6222 
         128          870           NA           NA         1000         1160 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1057          984           NA           NA           NA          814 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
        1006          508          693         2562          358         1662 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1152          798         1777         1521           NA         1050 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6481 TCGA-CR-6482 
        1125           NA          514           NA          311          345 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         354          233          379          350          479           NA 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
        1435         1190         1440         1244           NA          104 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
          NA          759          889           30          972           NA 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
        1036           NA          796           NA          997         1430 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
          NA          392          907          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
         898          929          216          156          180         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
         910         1471         4115          522         3930         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
        1438          584          546         2732         2663         2326 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
        2567         1969          519          406          540         1736 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
        1478         1007          215         1315         1246          405 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
         743          179           NA           NA           NA           NA 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
          NA           NA           NA           NA           NA         3835 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
          NA           NA           NA         3836         3380           NA 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
          NA           NA           NA           NA         3496         1724 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
          NA         1444         1095          953          797           NA 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 
        1099           NA           NA           NA           NA           NA 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
          NA           NA           NA           NA           NA         4334 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
          NA           NA           NA          316          321          236 
TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
         828          403          325          250          238           77 
TCGA-D6-6825 TCGA-D6-6826 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         152          153         1149         1058          516          477 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
         548           NA          575          661          360          299 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-H7-7774 TCGA-HD-7229 
         369          368          324           35           30            2 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-IQ-7630 
           5           25           NA           NA           31          160 
TCGA-IQ-7631 TCGA-IQ-7632 
         122          113 
Variable 1:'AGE':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=115,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=197,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=94,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'PATHOLOGY.T':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'PATHOLOGY.N':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'PATHOLOGICSPREAD(M)':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'TUMOR.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBERPACKYEARSSMOKED':	nDistinctValues=68,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "GENDER"                                
 [3] "PATHOLOGY.T"                           
 [4] "PATHOLOGY.N"                           
 [5] "TUMOR.STAGE"                           
 [6] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [7] "NUMBERPACKYEARSSMOKED"                 
 [8] "TOBACCOSMOKINGHISTORYINDICATOR"        
 [9] "YEAROFTOBACCOSMOKINGONSET"             
[10] "NUMBER.OF.LYMPH.NODES"                 
[1] "TUMOR.?STAGE" "5"           
[1] "stage2"
vv
  1   2   3   4 
 16  47  41 153 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 302 columns, 1 survival variables, and 10 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
CYB5B|80777 
       4212 
AGE, nv=56, binary=FALSE, numeric=TRUE
RNASE3|6037 
      13525 
GENDER, nv=2, binary=FALSE, numeric=FALSE
XIST|7503 
    17541 
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
LRRC8A|56262 
        9470 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
 T1  T2  T3  T4 
 23  78  60 101 
PATHOLOGY.N, nv=4, binary=FALSE, numeric=TRUE
SPRR2F|6705 
      15256 
[1] "PATHOLOGY.N"
[1] "num to class table"
vv1
 N0  N1  N2  N3 
100  32  97   5 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
PTDSS1|9791 
      12861 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
     16      47      41     153 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
ITPRIPL2|162073 
           8024 
NUMBERPACKYEARSSMOKED, nv=68, binary=FALSE, numeric=TRUE
GLI2|2736 
     6544 
TOBACCOSMOKINGHISTORYINDICATOR, nv=4, binary=FALSE, numeric=FALSE
THAP11|57215 
       15967 
YEAROFTOBACCOSMOKINGONSET, nv=52, binary=FALSE, numeric=TRUE
DNASE1L1|1774 
         4724 
NUMBER.OF.LYMPH.NODES, nv=26, binary=FALSE, numeric=TRUE
ARL4C|10123 
        947 
> q(save="no")
