
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/GDAC_RPPA_preprocess/HNSC-TP/3026014/0.GDAC_RPPA_preprocess.Finished/HNSC-TP.rppa.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=212, common to both=212
Number of genes in original expression dataset=174
[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 212 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
         461          276          248          190          845         1761 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6870 
         186          179          242         1747          244           NA 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BB-4217 TCGA-CN-4722 TCGA-CN-4723 
          63           NA          113          186          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-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CQ-5323 
         119           NA          114          100           46         1465 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1207          654           NA         1183          841          896 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 
        1028          317          128          870           NA           NA 
TCGA-CQ-6221 TCGA-CQ-6222 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
        1000         1160          984           NA           NA           NA 
TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
         814         1006          693         4115          522         3930 
TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
        3295          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-7425 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-CV-7446 TCGA-CV-7568 TCGA-CX-7085 
          NA           NA           NA           NA           NA          321 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
         236          828          403          325          250          238 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-DQ-7591 TCGA-DQ-7592 
          77          152          153          127          360          299 
TCGA-IQ-7630 TCGA-IQ-7632 
         160          113 
Variable 1:'AGE':	nDistinctValues=50,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=102,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=124,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=2,	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=83,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'PATHOLOGY.T':	nDistinctValues=5,	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=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'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] "NUMBERPACKYEARSSMOKED"                 
 [8] "TOBACCOSMOKINGHISTORYINDICATOR"        
 [9] "YEAROFTOBACCOSMOKINGONSET"             
[10] "NUMBER.OF.LYMPH.NODES"                 
[1] "TUMOR.?STAGE" "5"           
[1] "stage2"
vv
  1   2   3   4 
  9  39  31 121 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 212 columns, 1 survival variables, and 10 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
SMAD3|SMAD3-R-V 
            128 
AGE, nv=50, binary=FALSE, numeric=TRUE
CASP8|CASPASE-8-M-C 
                 38 
GENDER, nv=2, binary=FALSE, numeric=FALSE
MAPK14|P38_PT180_Y182-R-V 
                      170 
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
MAPK1 MAPK3|MAPK_PT202_Y204-R-V 
                             86 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
T1 T2 T3 T4 
13 59 53 79 
PATHOLOGY.N, nv=4, binary=FALSE, numeric=TRUE
SRC|SRC_PY416-R-C 
              132 
[1] "PATHOLOGY.N"
[1] "num to class table"
vv1
N0 N1 N2 N3 
73 20 79  4 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
MAPK1 MAPK3|MAPK_PT202_Y204-R-V 
                             86 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
      9      39      31     121 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
BCL2|BCL-2-R-C 
            23 
NUMBERPACKYEARSSMOKED, nv=46, binary=FALSE, numeric=TRUE
CHEK2|CHK2-M-C 
            43 
TOBACCOSMOKINGHISTORYINDICATOR, nv=4, binary=FALSE, numeric=FALSE
NOTCH1|NOTCH1-R-V 
               96 
YEAROFTOBACCOSMOKINGONSET, nv=46, binary=FALSE, numeric=TRUE
RPS6|S6-R-C 
        120 
NUMBER.OF.LYMPH.NODES, nv=23, binary=FALSE, numeric=TRUE
ANXA1|ANNEXIN_I-R-V 
                 19 
> q(save="no")
