
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.14.3949/ClinicalAnalysisAllGenes.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ClinicalAnalysisAllGenes_new.14.3949/", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/COADREAD-TP/2904206/0.GDAC_MethylationPreprocess.Finished/COADREAD-TP.meth.for_correlation.filtered_data.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=588, in expression file=239, common to both=239
Number of genes in original expression dataset=17147
[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 239 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-A6-2675 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-4105 TCGA-A6-5656 
         515          424          387          464          441          462 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
         286          342          306          297          362          286 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
         244          320          181          124          129          133 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
         172          248          134           90          177           86 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 
         158          164           31           NA           31           31 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3509 TCGA-AA-3511 TCGA-AA-3655 TCGA-AA-3660 
          31           NA           NA           NA           NA           31 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3697 TCGA-AA-3713 TCGA-AD-5900 TCGA-AD-6548 
          NA           31           29           29            2            3 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
         128         1719           24           22           47           31 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
          30            6           14           28           NA           40 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4313 TCGA-AZ-4315 
         230            6          112          162          957         1334 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-5403 
          NA          172          505           NA         1705           NA 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        1395           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-4947 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
         533         1491          474         1461          853          669 
TCGA-CK-5915 TCGA-CK-5916 TCGA-CK-6746 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
          NA           NA           NA           89           61         3134 
TCGA-CM-4743 TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
         184          244          607          304          393          335 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
         304          335           NA          304           61          304 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
         212          212           90          424          122          181 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
         242          181          211          149          152          152 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
         152          122          122          456          204           30 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 
         198          202          271           17           40          241 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
          10          287          136          246          144          186 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
          88           95           67           20          145           45 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
        3429          743         1162         3621         2821         1518 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-F4-6459 
          NA          383         3927          227         1348           NA 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
          NA           NA           NA           NA           NA           56 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
          46           16           20           16           14           38 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
          42           20         3203          254         2288           NA 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 
        1309         1631         1358         1386         1112         1031 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
         937          893          678          571          741          644 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2693 
        2672           NA         1611          594          358          581 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3591 TCGA-AG-3732 TCGA-AG-3742 
         536          441          231           NA           NA           30 
TCGA-AG-4022 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6623 
          30            6           21           22          140          285 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
         143         1825          243          304          153          273 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
         212          849          212          608          121          152 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
           8         3635         3683          734          991           15 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
         121           83          159          237           84           62 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
          26           66           12           31           20           21 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
          16           33           23           14         1451 
Variable 1:'AGE':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=154,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=2,	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=58,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'PATHOLOGY.T':	nDistinctValues=7,	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=12,	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=23,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=12,	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 
41 90 64 32 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "5"          
[1] "PATHOLOGY.N" "6"          
Output Data has 239 columns, 1 survival variables, and 11 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
MORC2 
 9451 
AGE, nv=56, binary=FALSE, numeric=TRUE
GDNF 
6022 
PRIMARY.SITE.OF.DISEASE, nv=2, binary=FALSE, numeric=FALSE
 PAK2 
10727 
GENDER, nv=2, binary=FALSE, numeric=FALSE
KIF4B 
 7851 
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
METTL3 
  9241 
PATHOLOGY.T, nv=5, binary=FALSE, numeric=TRUE
TIMP4 
14948 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
 T0  T1  T2  T3  T4 
  1   8  41 155  34 
PATHOLOGY.N, nv=3, binary=FALSE, numeric=TRUE
UBE2L6 
 15840 
[1] "PATHOLOGY.N"
[1] "num to class table"
vv1
 N0  N1  N2 
141  55  40 
PATHOLOGICSPREAD(M), nv=5, binary=FALSE, numeric=FALSE
JOSD2 
 7516 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
UBE2L6 
 15840 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
     41      90      64      32 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
SFRS13B 
  13335 
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
GGCT 
6050 
NUMBER.OF.LYMPH.NODES, nv=23, binary=FALSE, numeric=TRUE
CASP1 
 2607 
> q(save="no")
