
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/miRseq_preprocessor/LUSC-TP/2859878/0.miRseq_preprocessor.Finished/LUSC-TP.miRseq_RPKM_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LUSC-TP/2843850/1.GDAC_clinicalDataPicker.Finished/LUSC-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=327, in expression file=349, common to both=300
Number of genes in original expression dataset=548
[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 300 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
         370          136         2466          146         1415          345 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
         396         1810          862          758           49         1331 
TCGA-18-4086 TCGA-18-4721 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
          85         2753         3016         2133         1852         1058 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 
         473          964         3724          267          962           NA 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1011 
         908          656          329          608          223           53 
TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 
         429          622         1067         1470          734           17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 
        1057          399           NA          587           NA          358 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
         964         1974         1932          444         1345           24 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
        1651         2170           NA          357          573          915 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 
        1912         1713          505         2524         3469         2979 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
        1311         5286         3149         4299          428           NA 
TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 
         334           NA          821           80         1874          958 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
         881          999          950         1528         1575          994 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
          NA          329          235          428          698          168 
TCGA-34-5929 TCGA-34-7107 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 
          NA           NA          120           13           12          246 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5019 
         238          207           12          103         1454         1360 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
        2086           NA         2130         1848           52          740 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
          59          832         1107          474         1084           24 
TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
         544          556          550          399          352          573 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
         258          549          213          183           85           NA 
TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
          NA          212           48         2023          202          193 
TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 
          NA           NA           NA           NA           NA           29 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-51-6867 TCGA-52-7622 
          18           12           12           63           NA          541 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
         178          922           NA           NA          880            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-56-7730 TCGA-56-7822 TCGA-60-2695 
          44           40           26            6            1          473 
TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
         109           NA          311           NA           NA         2500 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
        2082         1505         1685          888          274         1456 
TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 
         512         1181          931           96          793          733 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-5128 TCGA-63-5131 TCGA-63-6202 
         693           37          719           NA           NA           NA 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 
          NA           NA           NA          516         1311           61 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2758 
         641           30           31           61           28          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-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
         700          578           61          366          121          365 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
         759           59          790         1217          699          123 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
         699          153          913          306         1645          122 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
        1492           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-85-8287 TCGA-85-8288 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
          13           44           54           41           47           89 
TCGA-90-7769 TCGA-90-7964 TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
          18          100           82          106          122          160 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-96-7544 TCGA-96-7545 
          69           87           NA          143         1213         1777 
TCGA-96-8169 TCGA-96-8170 TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
         188          210          115          413          223          308 
Variable 1:'AGE':	nDistinctValues=43,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=106,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=206,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=6,	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=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=135,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'PATHOLOGY.T':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'PATHOLOGY.N':	nDistinctValues=5,	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=83,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=16,	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 
153  83  58   3 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "5"          
[1] "PATHOLOGY.N" "6"          
Output Data has 300 columns, 1 survival variables, and 13 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
HSA-MIR-556 
        459 
AGE, nv=43, binary=FALSE, numeric=TRUE
HSA-MIR-125A 
          44 
GENDER, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-375 
        330 
KARNOFSKY.PERFORMANCE.SCORE, nv=8, binary=FALSE, numeric=TRUE
HSA-LET-7G 
        10 
HISTOLOGICAL.TYPE, nv=5, binary=FALSE, numeric=FALSE
HSA-MIR-29A 
        207 
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
HSA-MIR-150 
        104 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
 T1  T2  T3  T4 
 72 181  31  16 
PATHOLOGY.N, nv=4, binary=FALSE, numeric=TRUE
HSA-MIR-30A 
        215 
[1] "PATHOLOGY.N"
[1] "num to class table"
vv1
 N0  N1  N2  N3 
183  85  26   4 
PATHOLOGICSPREAD(M), nv=3, binary=FALSE, numeric=FALSE
HSA-MIR-26A-1 
          199 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
HSA-MIR-497 
        399 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
    153      83      58       3 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-3622A 
          298 
NUMBERPACKYEARSSMOKED, nv=83, binary=FALSE, numeric=TRUE
HSA-MIR-136 
         86 
TOBACCOSMOKINGHISTORYINDICATOR, nv=4, binary=FALSE, numeric=FALSE
HSA-MIR-3926-1 
           352 
YEAROFTOBACCOSMOKINGONSET, nv=48, binary=FALSE, numeric=TRUE
HSA-MIR-125A 
          44 
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
HSA-MIR-3607 
         286 
> q(save="no")
