
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/COADREAD-TP/2843420/0.GDAC_RPPA_preprocess.Finished/COADREAD-TP.rppa.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/COADREAD-TP/2843108/1.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=399, common to both=399
Number of genes in original expression dataset=171
[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] "COMPLETENESS.OF.RESECTION"             
[17] "NUMBER.OF.LYMPH.NODES"                 
[18] "BATCHNUMBER"                           

Input Data has 18 rows and 399 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 
         648          503          447          541          437          522 
TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
         552          472          387          464          488          332 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
         278          313          246          462          367          286 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
         342          306          297          362          286          244 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
         320          195          181          124          129          133 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
         253          146          172          248          134           90 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
         177           86          158          164           31           NA 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
          31           31           NA           31           NA           NA 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3521 TCGA-AA-3522 TCGA-AA-3525 
          NA           NA           NA           NA           NA           NA 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3548 
          NA           NA           NA           NA           NA           NA 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 
          NA           NA           NA           30           NA           NA 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3678 
          NA           31           NA           NA           NA           NA 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3695 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
          NA           NA           NA           NA           29           31 
TCGA-AA-3712 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3814 
          NA           29           30           30           NA           NA 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
          NA           NA           NA           NA           NA           31 
TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 
          NA           28           NA           30           NA           NA 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3861 TCGA-AA-3862 TCGA-AA-3864 TCGA-AA-3866 
          31           NA           NA           31           NA           NA 
TCGA-AA-3869 TCGA-AA-3872 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3955 
          NA           NA           NA           30           31           NA 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 
          NA           NA           NA           NA           30           NA 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6899 
          30           NA            2            3         1719           47 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 
           6           14           28           40          230            6 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
         112          162         1714         1334           NA          172 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 
         505           NA          680         1705         1395           NA 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
          NA           NA           NA           NA           NA           NA 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
          NA           NA            5            2           NA           12 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
           8            2            8           10            3           41 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6746 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
         669           NA           NA           89           61         3134 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
         184          214          699          244          214          244 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
         123          183          304          393          335          304 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
         335           NA          304           61          304          212 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
         212           90          487          212          424          122 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
         181          243          242          181          211          149 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
         152          152          152          122          122           91 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
         204           30          198          202          260          271 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
          17          107           40          241           10          287 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
         136          246          144          186          108           45 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
         111          133           42           88           95           67 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-F4-6459 TCGA-F4-6460 
          20           45           43           19           NA           NA 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
          NA           NA           NA           NA           56           46 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
          16           20           16           14           38           16 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
          42           20         3203          858          254         2288 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
          NA         2077         1309         1882         1631         1358 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
        1485         1386         1204         1112         1031          937 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
         893          678          571          546          201          741 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-AF-2689 
         644         2672           NA         1434         1611          482 
TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-3914 TCGA-AF-5654 TCGA-AF-6136 
         358          387          316          264          257          231 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
         193          223           NA           NA           NA           31 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
          31           61           NA           NA           31           NA 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3601 
          NA           NA           NA           30           NA           NA 
TCGA-AG-3602 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3727 
          NA           NA           NA           NA           NA           29 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 
          31           30           30           NA           NA           NA 
TCGA-AG-3891 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
          30           30           NA           NA           NA           NA 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4015 TCGA-AG-4021 
          31           NA           31           31           NA           NA 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
          30          637          423          183          789          700 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
         518          484          396           31           31          365 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G 
        2130         1946          334           NA           NA           NA 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
        1884         1246         2192           15           44            6 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6621 TCGA-CL-5918 
          21           22          140          310           NA          243 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 
         334          335          304          153          224          212 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
         849          212          608          180          121          152 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
           8         3635         1257         1741         3683          734 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
        1566          991           15           73          232            5 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
          66          250           14          121           20          210 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
         216          187          108           83          159          237 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
          NA          103           26           66           12           31 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
          20           21           33           23           14           NA 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        1451           NA          636 
Variable 1:'AGE':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=30,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=195,	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=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=72,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'PATHOLOGY.T':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'PATHOLOGY.N':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'PATHOLOGICSPREAD(M)':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=30,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=19,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "PRIMARY.SITE.OF.DISEASE"               
 [3] "GENDER"                                
 [4] "HISTOLOGICAL.TYPE"                     
 [5] "PATHOLOGY.T"                           
 [6] "PATHOLOGY.N"                           
 [7] "PATHOLOGICSPREAD(M)"                   
 [8] "TUMOR.STAGE"                           
 [9] "RADIATIONS.RADIATION.REGIMENINDICATION"
[10] "COMPLETENESS.OF.RESECTION"             
[11] "NUMBER.OF.LYMPH.NODES"                 
[1] "TUMOR.?STAGE" "8"           
[1] "stage2"
vv
  1   2   3   4 
 61 147 119  57 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "5"          
[1] "PATHOLOGY.N" "6"          
Output Data has 399 columns, 1 survival variables, and 11 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
XBP1|XBP1-G-C 
          141 
AGE, nv=59, binary=FALSE, numeric=TRUE
RB1|RB_PS807_S811-R-V 
                  117 
PRIMARY.SITE.OF.DISEASE, nv=2, binary=FALSE, numeric=FALSE
CHEK1|CHK1_PS345-R-C 
                  41 
GENDER, nv=2, binary=FALSE, numeric=FALSE
BRAF|B-RAF-M-NA 
             19 
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
CHEK1|CHK1_PS345-R-C 
                  41 
PATHOLOGY.T, nv=5, binary=FALSE, numeric=TRUE
ERRFI1|MIG-6-M-V 
              88 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
 T0  T1  T2  T3  T4 
  1   9  68 276  41 
PATHOLOGY.N, nv=3, binary=FALSE, numeric=TRUE
EIF4E|EIF4E-R-V 
            158 
[1] "PATHOLOGY.N"
[1] "num to class table"
vv1
 N0  N1  N2 
224 103  68 
PATHOLOGICSPREAD(M), nv=5, binary=FALSE, numeric=FALSE
IGFBP2|IGFBP2-R-V 
               76 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
GAB2|GAB2-R-V 
           65 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
     61     147     119      57 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
PECAM1|CD31-M-V 
             31 
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
PIK3CA|PI3K-P110-ALPHA-R-C 
                       102 
NUMBER.OF.LYMPH.NODES, nv=30, binary=FALSE, numeric=TRUE
GAB2|GAB2-R-V 
           65 
> q(save="no")
