
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/mRNAseq_preprocessor/COADREAD-TP/2282096/0.mRNAseq_preprocessor.Finished/COADREAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/COADREAD-TP/2172432/1.GDAC_clinicalDataPicker.Finished/COADREAD-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=591, in expression file=264, common to both=264
Number of genes in original expression dataset=17880
[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] "HISTOLOGICALTYPE"                      
[11] "PATHOLOGICSPREAD(PT)"                  
[12] "PATHOLOGICSPREAD(PN)"                  
[13] "PATHOLOGICSPREAD(M)"                   
[14] "TUMORSTAGE"                            
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 264 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-A6-2670 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 
         423          648          503          523          447          541 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
         437          595          522          552          424          472 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 
         387          464          332          278          313          246 
TCGA-A6-4107 TCGA-AA-3488 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
         231           91           NA           31           31           31 
TCGA-AA-3506 TCGA-AA-3509 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
          NA           NA           NA           NA           NA           31 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3521 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
          NA           NA           NA           NA           NA           NA 
TCGA-AA-3527 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
          NA           NA           NA           NA           NA           NA 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
          NA           NA           NA           NA           NA           NA 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 
          NA           NA           NA           30           NA           NA 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
          NA           31           NA           31           NA           NA 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3684 
          NA           NA           30           NA           NA           NA 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3693 TCGA-AA-3695 TCGA-AA-3696 TCGA-AA-3710 
          NA           NA           NA           NA           NA           31 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3814 TCGA-AA-3815 TCGA-AA-3818 
          30           30           NA           NA           NA           NA 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
          NA           NA           NA           NA           31           NA 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
          31           28           NA           30           30           NA 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
          NA           NA           31           NA           NA           NA 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3862 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
          NA           NA           31           NA           NA           NA 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3872 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
          NA           NA           NA           NA           30           NA 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
          30           31           30           30           31           31 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3970 TCGA-AA-3971 
          NA           NA           31           NA           NA           NA 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
          NA           NA           30           NA           31           NA 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3984 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
          NA           NA           NA           30           NA           NA 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
         424          548          578          913         1035          548 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
         548          517          122          822          822           30 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
         517          456          669          638          457          457 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
          30          396          365          365          396         1158 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
          31         1065           31         1005         1065          791 
TCGA-AA-A01Z TCGA-AA-A022 TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
         638           NA         1188         1580           89         1215 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F 
          61          153           28          670         1246          548 
TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
        1245          496           29         1714          957         1334 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-CA-5256 TCGA-CK-4951 
         172          505         2180         1705           NA         1491 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
         699          244          214          244          123          183 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 
         323          412          387          316           NA           NA 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
          NA           NA           31           31           61           NA 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
          NA           31           NA           NA           NA           30 
TCGA-AG-3600 TCGA-AG-3601 TCGA-AG-3602 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
          NA           NA           NA           NA           NA           NA 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3878 
          NA           NA           31           29           NA           30 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
          NA           NA           NA           NA           28           NA 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
          31           30           30           NA           NA           NA 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
          NA           31           31           NA           31           31 
TCGA-AG-4015 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
          NA          637          423          183          789          700 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
         518          484          396           31           31          365 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
         365         2130         1946          334         1581         1519 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
          59         1184         1884         1246         1156         2192 
Variable 1:'AGE':	nDistinctValues=50,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=83,	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=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=82,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'PATHOLOGY.T':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'PATHOLOGY.N':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'PATHOLOGICSPREAD(M)':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                     "PRIMARY.SITE.OF.DISEASE"
[3] "GENDER"                  "HISTOLOGICAL.TYPE"      
[5] "PATHOLOGY.T"             "PATHOLOGY.N"            
[7] "PATHOLOGICSPREAD(M)"     "TUMOR.STAGE"            
[1] "TUMOR.?STAGE" "8"           
[1] "stage2"
vv
 1  2  3  4 
53 98 68 37 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "5"          
[1] "PATHOLOGY.N" "6"          
Output Data has 264 columns, 1 survival variables, and 8 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
ACTN2|88 
     207 
AGE, nv=50, binary=FALSE, numeric=TRUE
TMEM229B|161145 
          15798 
PRIMARY.SITE.OF.DISEASE, nv=2, binary=FALSE, numeric=FALSE
DRD5|1816 
     4656 
GENDER, nv=2, binary=FALSE, numeric=FALSE
RPS4Y1|6192 
      13328 
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
SNHG11|128439 
        14504 
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
NRG1|3084 
    10745 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
 T1  T2  T3  T4 
 11  53 176  22 
PATHOLOGY.N, nv=3, binary=FALSE, numeric=TRUE
DIRAS2|54769 
        4423 
[1] "PATHOLOGY.N"
[1] "num to class table"
vv1
 N0  N1  N2 
158  57  48 
PATHOLOGICSPREAD(M), nv=3, binary=FALSE, numeric=FALSE
GFI1|2672 
     6246 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
GFI1|2672 
     6246 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
     53      98      68      37 
> q(save="no")
