
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/3140905/0.GDAC_MethylationPreprocess.Finished/LUSC-TP.meth.for_correlation.filtered_data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LUSC-TP/3132702/1.GDAC_clinicalDataPicker.Finished/LUSC-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=324, in expression file=218, common to both=187
Number of genes in original expression dataset=17536
[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] "PATHOLOGICSPREAD(PT)"                  
[13] "PATHOLOGICSPREAD(PN)"                  
[14] "PATHOLOGICSPREAD(M)"                   
[15] "TUMORSTAGE"                            
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "NUMBERPACKYEARSSMOKED"                 
[18] "TOBACCOSMOKINGHISTORYINDICATOR"        
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "COMPLETENESS.OF.RESECTION"             
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 187 columns.

[1] "Batch" "21"   
[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          656          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-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 
         258          213          183           85           NA           NA 
TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-46-6025 TCGA-46-6026 TCGA-51-6867 
         212          202          193           29           18           NA 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 
         541          178          922           NA           NA            3 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
          NA           62           31           30           13           30 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7822 TCGA-60-2697 TCGA-60-2703 
          44           40           26            1           NA           NA 
TCGA-60-2704 TCGA-60-2709 TCGA-63-5128 TCGA-63-5131 TCGA-63-6202 TCGA-63-7020 
          NA         1505           NA           NA           NA           NA 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-68-7755 TCGA-68-7756 TCGA-68-8251 
          NA           NA           NA           83          202           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-90-6837 TCGA-90-7766 
          13           11           44           54           41           47 
TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
          89           18          100           82          106          122 
TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-96-7544 
         160           69           87           NA          143         1213 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
        1777          188          210          115          413          223 
TCGA-98-8023 
         308 
Variable 1:'AGE':	nDistinctValues=41,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=68,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=120,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=5,	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:'PATHOLOGY.T':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'PATHOLOGY.N':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'PATHOLOGICSPREAD(M)':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TUMOR.STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBERPACKYEARSSMOKED':	nDistinctValues=62,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'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] "PATHOLOGY.T"                           
 [6] "PATHOLOGY.N"                           
 [7] "PATHOLOGICSPREAD(M)"                   
 [8] "TUMOR.STAGE"                           
 [9] "RADIATIONS.RADIATION.REGIMENINDICATION"
[10] "NUMBERPACKYEARSSMOKED"                 
[11] "TOBACCOSMOKINGHISTORYINDICATOR"        
[12] "YEAROFTOBACCOSMOKINGONSET"             
[13] "COMPLETENESS.OF.RESECTION"             
[1] "TUMOR.?STAGE" "8"           
[1] "stage2"
vv
 1  2  3  4 
92 60 31  1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "5"          
[1] "PATHOLOGY.N" "6"          
Output Data has 187 columns, 1 survival variables, and 13 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
ACN9 
 145 
AGE, nv=41, binary=FALSE, numeric=TRUE
EML4 
4954 
GENDER, nv=2, binary=FALSE, numeric=FALSE
KIF4B 
 8025 
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
MEPCE 
 9453 
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
SETDB2 
 13625 
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
ZNF45 
17202 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
 T1  T2  T3  T4 
 52 106  22   7 
PATHOLOGY.N, nv=3, binary=FALSE, numeric=TRUE
CCL7 
2913 
[1] "PATHOLOGY.N"
[1] "num to class table"
vv1
 N0  N1  N2 
113  57  15 
PATHOLOGICSPREAD(M), nv=3, binary=FALSE, numeric=FALSE
 PECR 
11309 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
CCL7 
2913 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
     92      60      31       1 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
UNC13A 
 16321 
NUMBERPACKYEARSSMOKED, nv=62, binary=FALSE, numeric=TRUE
ZNF234 
 17069 
TOBACCOSMOKINGHISTORYINDICATOR, nv=4, binary=FALSE, numeric=FALSE
TP53I3 
 15753 
YEAROFTOBACCOSMOKINGONSET, nv=44, binary=FALSE, numeric=TRUE
CPS1 
3776 
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
DDX54 
 4263 
> q(save="no")
