
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/1676634/0.mRNAseq_preprocessor.Finished/HNSC.uncv2.mRNAseq_RSEM_normalized_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/HNSC/1669666/1.GDAC_clinicalDataPicker.Finished/HNSC.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=311, in expression file=229, common to both=229
Number of genes in original expression dataset=18327
[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] "NEOADJUVANTTHERAPY"                    
[17] "BATCHNUMBER"                           

Input Data has 17 rows and 229 columns.

[1] "Batch" "17"   
[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          489          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5559 TCGA-BA-6868 
         190          845         1761          186         1747          152 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
         244           NA           63           NA          113          236 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-CN-4723 
         186         2891          275          140          557          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-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
         383          395          240          436          348          810 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
         875          397          279          289          173          377 
TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5370 TCGA-CN-5374 
         866          193          252          493           NA          274 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6018 
         207          228          143          154          201           45 
TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
         134          276          201          188          224           42 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6997 TCGA-CQ-5323 
         177           83          119           NA          100         1465 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 
        1207          654           NA          841          896          317 
TCGA-CQ-5334 TCGA-CQ-6222 TCGA-CQ-6224 TCGA-CQ-7068 TCGA-CR-5243 TCGA-CR-5247 
         128         1160          984          693         2562          358 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
        1662         1152          798         1777         1521           NA 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6481 
        1050         1125           NA          514           NA          311 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 
         345          354          233          379          479           NA 
TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 
        1435         1244           NA          104           NA          889 
TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
          30           NA         1036           NA          796           NA 
TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7392 TCGA-CR-7393 
         997           NA          392          907          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-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
          NA         3835           NA           NA           NA           NA 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        3836         3380           NA           NA           NA           NA 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
        1724           NA         1444          797           NA           NA 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 
          NA           NA           NA           NA         1099           NA 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7437 
          NA           NA           NA           NA         4334           NA 
TCGA-CV-7438 TCGA-CV-7440 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
          NA           NA          316          321          236          828 
TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6823 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
         403          250          238         1149         1058          516 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-7848 
         477          548           NA          360          299           35 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7832 TCGA-IQ-7630 TCGA-IQ-7631 
           2            5           25           NA          160          122 
TCGA-IQ-7632 
         113 
Variable 1:'AGE':	nDistinctValues=53,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=94,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=156,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	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=82,	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:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'BATCH.NUMBER':	nDistinctValues=8,	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] "NEOADJUVANT.THERAPY"                   
[1] "TUMOR.?STAGE" "5"           
[1] "stage2"
vv
  1   2   3   4 
  9  34  29 121 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 229 columns, 1 survival variables, and 7 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
CYB5B|80777 
       4188 
AGE, nv=53, binary=FALSE, numeric=TRUE
RNASE3|6037 
      13476 
GENDER, nv=2, binary=FALSE, numeric=FALSE
XIST|7503 
    17485 
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
SAMD8|142891 
       13920 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
T1 T2 T3 T4 
12 55 47 82 
PATHOLOGY.N, nv=4, binary=FALSE, numeric=TRUE
ADAMTSL5|339366 
            282 
[1] "PATHOLOGY.N"
[1] "num to class table"
vv1
N0 N1 N2 N3 
73 23 76  3 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
SAMD8|142891 
       13920 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
      9      34      29     121 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
ITPRIPL2|162073 
           7987 
NEOADJUVANT.THERAPY, nv=2, binary=FALSE, numeric=FALSE
NBPF14|25832 
       10619 
> q(save="no")
