
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/LUSC-TP/3527745/LUSC-TP.meth.by_min_expr_corr.data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/LUSC-TP/3351655/LUSC-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=348, in expression file=252, common to both=203
Number of genes in original expression dataset=20217
[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] "KARNOFSKYPERFORMANCESCORE"             
[11] "HISTOLOGICALTYPE"                      
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "NUMBERPACKYEARSSMOKED"                 
[14] "YEAROFTOBACCOSMOKINGONSET"             
[15] "DISTANT.METASTASIS"                    
[16] "LYMPH.NODE.METASTASIS"                 
[17] "COMPLETENESS.OF.RESECTION"             
[18] "TUMOR.STAGECODE"                       
[19] "NEOPLASM.DISEASESTAGE"                 
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 203 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-18-3417 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-5782 TCGA-21-5783 
         758         2753           92          826          962           NA 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-4593 TCGA-22-4599 TCGA-22-4601 
         908          661          329         1067         1161         1057 
TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
          NA           NA          358          964         1974         1932 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
         444         1345           24         1651         2170           NA 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
         357          573          915         1912         1713          505 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 
        5286         3149         4299          428           NA          334 
TCGA-33-6737 TCGA-33-6738 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
          NA          821         1528         1575          994           NA 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
         329          235          428          698          168           NA 
TCGA-34-7107 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
          NA          103         1454         2253         1360         2086 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
          NA         2130         1848           52          740           59 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 
         832         1107          474         1084           24          544 
TCGA-39-5040 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
          NA          258          549          213          183           85 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
          NA           NA          212           48         2023          202 
TCGA-43-8116 TCGA-46-6025 TCGA-46-6026 TCGA-51-6867 TCGA-52-7622 TCGA-52-7809 
         193           29           18           NA          541           NA 
TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
         922           NA           NA            3           NA           62 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
          31           30           13           30           44           40 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7822 TCGA-56-8504 TCGA-56-8624 TCGA-56-8626 
          26            6            1          177           36           17 
TCGA-56-8628 TCGA-56-8629 TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2709 
          16           34           NA           NA           NA         1505 
TCGA-63-5128 TCGA-63-5131 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
          NA           NA           NA           NA           NA           NA 
TCGA-63-7023 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
          NA           83          202          211          244           95 
TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
          NA           NA           NA           NA           NA           NA 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
          NA         2736           NA           15         1285           NA 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 
          NA           NA           NA          479           NA           NA 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
        1641           NA         2522           NA           NA           NA 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 
          NA         3166           NA           NA          833           NA 
TCGA-77-8146 TCGA-77-8148 TCGA-77-8150 TCGA-77-8154 TCGA-77-8156 TCGA-79-5596 
        2183          293           NA         1092           10           NA 
TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
          NA           11           24           34           18           10 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
          49            1           NA           35           38           60 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 
          26           60           16           43           14           36 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-A4QR TCGA-90-6837 
          13           11           44           54           25           41 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE 
          47           89           18          100          244          331 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
          82          106          122          160           69           87 
TCGA-94-7557 TCGA-94-7943 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 
          NA          143         1213         1323          188          210 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-L3-A4E7 
         115          413          223          308           35 
Variable 1:'AGE':	nDistinctValues=41,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=69,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=129,	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=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'NUMBERPACKYEARSSMOKED':	nDistinctValues=65,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'DISTANT.METASTASIS':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'LYMPH.NODE.METASTASIS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'TUMOR.STAGECODE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NEOPLASM.DISEASESTAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "GENDER"                                
 [3] "KARNOFSKY.PERFORMANCE.SCORE"           
 [4] "HISTOLOGICAL.TYPE"                     
 [5] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [6] "NUMBERPACKYEARSSMOKED"                 
 [7] "YEAROFTOBACCOSMOKINGONSET"             
 [8] "DISTANT.METASTASIS"                    
 [9] "LYMPH.NODE.METASTASIS"                 
[10] "COMPLETENESS.OF.RESECTION"             
[11] "TUMOR.STAGECODE"                       
[12] "NEOPLASM.DISEASESTAGE"                 
[1] "TUMOR.?STAGE" "11"          
[1] "stage2"
vv
 T1 T1A T1B  T2 T2A T2B  T3  T4 
 24  12  22  62  38  14  24   7 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 203 columns, 1 survival variables, and 12 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
MED12L__2 
    10613 
AGE, nv=41, binary=FALSE, numeric=TRUE
TSC22D4 
  18434 
GENDER, nv=2, binary=FALSE, numeric=FALSE
KIF4B 
 9018 
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
MEPCE 
10672 
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
SLC27A1 
  16169 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
 PNMT 
13620 
NUMBERPACKYEARSSMOKED, nv=65, binary=FALSE, numeric=TRUE
DPY19L2 
   5189 
YEAROFTOBACCOSMOKINGONSET, nv=46, binary=FALSE, numeric=TRUE
GRWD1 
 7415 
DISTANT.METASTASIS, nv=3, binary=FALSE, numeric=FALSE
ZNF30 
19764 
LYMPH.NODE.METASTASIS, nv=4, binary=FALSE, numeric=FALSE
CCDC53 
  3224 
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
CCDC42B__1 
      3213 
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
[1] "Clinical variable TUMOR.STAGECODE has too few non-missing values, n=0"
NEOPLASM.DISEASESTAGE, nv=9, binary=FALSE, numeric=FALSE
KIAA0101 
    8847 
> q(save="no")
