
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/LUSC/1973103/0.GDAC_RPPA_preprocess.Finished/LUSC.rppa.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LUSC/1971863/1.GDAC_clinicalDataPicker.Finished/LUSC.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=309, in expression file=195, common to both=190
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] "KARNOFSKYPERFORMANCESCORE"             
[11] "HISTOLOGICALTYPE"                      
[12] "PATHOLOGICSPREAD(PT)"                  
[13] "PATHOLOGICSPREAD(PN)"                  
[14] "PATHOLOGICSPREAD(M)"                   
[15] "TUMORSTAGE"                            
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "NEOADJUVANTTHERAPY"                    
[18] "BATCHNUMBER"                           

Input Data has 18 rows and 190 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
        2753           92          826         3516         1426         3016 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
        2133         1852          473          964         3724          283 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
        3644          267          962          908          656          329 
TCGA-22-0940 TCGA-22-1000 TCGA-22-1011 TCGA-22-4591 TCGA-22-4596 TCGA-22-4605 
         608          454           53          622           17           NA 
TCGA-22-4607 TCGA-22-4609 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
         587           NA          964         1974         1932          444 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 
        1345           24         1651         2170          357          573 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4547 
         915         1912         1713          505         2524         1311 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 
        5286         3149          428          334           NA          821 
TCGA-34-2596 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 
          80          958          881          999          950         1528 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 
        1575          994           NA          329          428          698 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
         168           NA           NA           13           12          199 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 
         238          207           12          103         1454         2253 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
        1360         2086           NA         2130         1848           52 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 
         740           59          832         1107          474           24 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
         550          399          352          258          549          213 
TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7658 TCGA-46-6025 TCGA-46-6026 
          85           NA          212         2023           29           18 
TCGA-51-6867 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
          NA           NA           NA            3           NA           62 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 
          31           30           13          473          109           NA 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 
         311           NA           NA         2500         2082         1505 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 
        1685          888          274         1456          512         1181 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
         931           96          793           37          719          358 
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-66-2727 TCGA-66-2737 TCGA-66-2758 TCGA-66-2766 TCGA-66-2767 
          NA          516           61          638           31           61 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
          61          215          700           92           61          578 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2788 TCGA-66-2790 
         121          365          759           59          699          699 
TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7756 TCGA-70-6722 
         153         1645          122         1492          202           NA 
TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 
          NA           NA           NA           NA           NA         2736 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
          15         1285           NA           NA           NA           NA 
TCGA-77-7465 TCGA-79-5596 TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 
         479           NA           NA           11           24           34 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
          18           10           49            1           NA           35 
TCGA-85-7844 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-92-7340 
          38           41           47           89           18           82 
TCGA-94-7033 TCGA-94-7557 TCGA-96-7544 TCGA-98-7454 
          87           NA         1213          115 
Variable 1:'AGE':	nDistinctValues=41,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=71,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=138,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=4,	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=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=102,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=8,	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=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TUMOR.STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'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] "NEOADJUVANT.THERAPY"                   
[1] "TUMOR.?STAGE" "8"           
[1] "stage2"
vv
 1  2  3 
96 55 36 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "5"          
[1] "PATHOLOGY.N" "6"          
Output Data has 190 columns, 1 survival variables, and 10 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
MSH6|MSH6-R-C 
           91 
AGE, nv=41, binary=FALSE, numeric=TRUE
PCNA|PCNA-M-V 
          100 
GENDER, nv=2, binary=FALSE, numeric=FALSE
NOTCH3|NOTCH3-R-C 
               97 
KARNOFSKY.PERFORMANCE.SCORE, nv=8, binary=FALSE, numeric=TRUE
FOXO3|FOXO3A-R-C 
              63 
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
EGFR|EGFR_PY1173-R-C 
                  56 
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
BID|BID-R-C 
         27 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
 T1  T2  T3  T4 
 43 117  19  11 
PATHOLOGY.N, nv=4, binary=FALSE, numeric=TRUE
MAPK1 MAPK3|MAPK_PT202_Y204-R-V 
                             86 
[1] "PATHOLOGY.N"
[1] "num to class table"
vv1
 N0  N1  N2  N3 
121  50  15   4 
PATHOLOGICSPREAD(M), nv=2, binary=FALSE, numeric=FALSE
CCNB1|CYCLIN_B1-R-V 
                 47 
TUMOR.STAGE, nv=3, 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 
     96      55      36 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
SETD2|SETD2-R-C 
            122 
NEOADJUVANT.THERAPY, nv=2, binary=FALSE, numeric=FALSE
AR|AR-R-V 
       12 
> q(save="no")
