
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.14.3949/ClinicalAnalysisAllGenes.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ClinicalAnalysisAllGenes_new.14.3949/", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/HNSC/1841475/0.GDAC_MethylationPreprocess.Finished/HNSC.meth.for_correlation.filtered_data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/HNSC/1708827/1.GDAC_clinicalDataPicker.Finished/HNSC.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=308, in expression file=286, common to both=283
Number of genes in original expression dataset=17460
[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 283 columns.

[1] "Batch" "17"   
[1] "Last Follow UP"
TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
         489          276          248          190          845         1761 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 
         186          179          242         1635         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-4722 
         186         2891          275          140          557          192 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
         412          310          142          194          325          166 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4736 
         343          383          522          226          369          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         240          436          348          810          875          397 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5361 
         279          289          173          377          866          193 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
         252          493          351          360          352          380 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
          NA          413          274          207          228          143 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         154          201          159           45          134           97 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
         276          201          188          224           42          177 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6997 TCGA-CN-6998 TCGA-CQ-5323 
          83          119           NA          100           46         1465 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654           NA          841          896         1028 
TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6221 
         317          128          870           NA           NA         1000 
TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
        1160         1057          984           NA           NA           NA 
TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
         814         1006          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-7410 TCGA-CV-7411 
        1099           NA           NA           NA           NA           NA 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 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-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
         403          325          250          238           77          152 
TCGA-D6-6826 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         153         1149         1058          516          477          548 
TCGA-DQ-7588 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-7848 TCGA-H7-7774 TCGA-HD-7229 
          NA          360          299           35           30            2 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-IQ-7630 TCGA-IQ-7631 
           5           25           NA           NA          160          122 
TCGA-IQ-7632 
         113 
Variable 1:'AGE':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=111,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=183,	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=91,	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 
 14  46  38 147 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 283 columns, 1 survival variables, and 7 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
ZNF266 
 17011 
AGE, nv=56, binary=FALSE, numeric=TRUE
SLC35D3 
  13996 
GENDER, nv=2, binary=FALSE, numeric=FALSE
KIF4B 
 7994 
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
LOC400657 
     8727 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
T1 T2 T3 T4 
20 75 57 98 
PATHOLOGY.N, nv=4, binary=FALSE, numeric=TRUE
SLC47A2 
  14060 
[1] "PATHOLOGY.N"
[1] "num to class table"
vv1
N0 N1 N2 N3 
94 31 93  4 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
LOC400657 
     8727 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
     14      46      38     147 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
ZCCHC17 
  16797 
NEOADJUVANT.THERAPY, nv=2, binary=FALSE, numeric=FALSE
ASRGL1 
   990 
> q(save="no")
