
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_mRNA_Preprocess_Median/LUSC-TP/3471935/LUSC-TP.medianexp.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=351, in expression file=154, common to both=154
Number of genes in original expression dataset=17814
[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 154 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2466         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
         345          396         1810          862          758           49 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
        1331          187           85         3516         1426         3016 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
        2133         1852         1058          473          964         3724 
TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
         283         3644          267          608          223          454 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 
         131         1953           53          429          822         1485 
TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
         622         1470          734           17         1161         1057 
TCGA-22-4604 TCGA-22-4607 TCGA-22-4613 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 
         399          587          358         2524         3469         2979 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4589 TCGA-34-2596 TCGA-34-2600 
        1311         5286         3149          334           80         1874 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5240 TCGA-34-5241 
         958          881          999          950          235          428 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
         120           13           12          199          246          227 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 
         238          207           12         1454         2253         2086 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
         740           59         1107          474         1084           24 
TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-46-3765 
         556          550          399          352          267           NA 
TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-51-4079 TCGA-51-4080 
          NA           NA           NA           NA           12           12 
TCGA-51-4081 TCGA-56-1622 TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2706 
          63          880          473          109          311         2500 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
         660         2082         1685          888          274         1456 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
         512         1075         1181          931           96          793 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-5128 
         733          693           37          719          358           NA 
TCGA-63-5131 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
          NA           NA         1311           61          641           30 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
          31           61           28           30           30          638 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
         761           30           61           31           61           61 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
          NA          700          578           NA           61          578 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
          NA          121           NA          759           59          790 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 
        1217          699           NA          699           NA          913 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
          NA         1645          122         1492 
Variable 1:'AGE':	nDistinctValues=35,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=60,	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=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=104,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'NUMBERPACKYEARSSMOKED':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=37,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'DISTANT.METASTASIS':	nDistinctValues=2,	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=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NEOPLASM.DISEASESTAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                         "GENDER"                     
 [3] "KARNOFSKY.PERFORMANCE.SCORE" "HISTOLOGICAL.TYPE"          
 [5] "NUMBERPACKYEARSSMOKED"       "YEAROFTOBACCOSMOKINGONSET"  
 [7] "DISTANT.METASTASIS"          "LYMPH.NODE.METASTASIS"      
 [9] "COMPLETENESS.OF.RESECTION"   "TUMOR.STAGECODE"            
[11] "NEOPLASM.DISEASESTAGE"      
[1] "TUMOR.?STAGE" "10"          
[1] "stage2"
vv
 T1 T1A T1B  T2 T2A  T3  T4 
 20   1   9  92   8  12  12 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 154 columns, 1 survival variables, and 11 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
METTL3 
  8878 
AGE, nv=35, binary=FALSE, numeric=TRUE
GIPC3 
 3130 
GENDER, nv=2, binary=FALSE, numeric=FALSE
RPS4Y1 
  2741 
KARNOFSKY.PERFORMANCE.SCORE, nv=5, binary=FALSE, numeric=TRUE
NFRKB 
 7025 
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "num to class table"
vv1
  0  50  70  90 100 
 18   2   1   4   1 
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
FAM5B 
 5689 
NUMBERPACKYEARSSMOKED, nv=55, binary=FALSE, numeric=TRUE
CNTD1 
  605 
YEAROFTOBACCOSMOKINGONSET, nv=37, binary=FALSE, numeric=TRUE
ALS2CR4 
    493 
DISTANT.METASTASIS, nv=2, binary=FALSE, numeric=FALSE
P2RY6 
 4005 
LYMPH.NODE.METASTASIS, nv=4, binary=FALSE, numeric=FALSE
C6ORF58 
  11451 
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
ANKRD33 
   3224 
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
[1] "Clinical variable TUMOR.STAGECODE has too few non-missing values, n=0"
NEOPLASM.DISEASESTAGE, nv=7, binary=FALSE, numeric=FALSE
 MYH4 
14328 
> q(save="no")
