
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/PANCAN12-TP/2432181/0.GDAC_MethylationPreprocess.Finished/PANCAN12-TP.meth.for_correlation.filtered_data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/PANCAN12-TP/2331464/1.GDAC_clinicalDataPicker.Finished/PANCAN12-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=4844, in expression file=238, common to both=238
Number of genes in original expression dataset=15521
[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] "RADIATIONTHERAPY"                                  
[11] "KARNOFSKYPERFORMANCESCORE"                         
[12] "EXAMINATIONS.EXAMINATION.KARNOFSKYPERFORMANCESCORE"
[13] "HISTOLOGICALTYPE"                                  
[14] "TUMORGRADE"                                        
[15] "PATHOLOGICSPREAD(PT)"                              
[16] "PATHOLOGICSPREAD(PN)"                              
[17] "PATHOLOGICSPREAD(M)"                               
[18] "TUMORSTAGE"                                        
[19] "PATIENTTUMORRECURRENCESTATUS"                      
[20] "DAYSTOTUMORRECURRENCE"                             
[21] "CHEMOTHERAPY"                                      
[22] "RADIATIONS.RADIATION.REGIMENINDICATION"            
[23] "NUMBERPACKYEARSSMOKED"                             
[24] "STOPPEDSMOKINGYEAR"                                
[25] "TOBACCOSMOKINGHISTORYINDICATOR"                    
[26] "YEAROFTOBACCOSMOKINGONSET"                         
[27] "BATCHNUMBER"                                       

Input Data has 27 rows and 238 columns.

[1] "Batch" "27"   
[1] "Last Follow UP"
TCGA-A1-A0SE TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO 
        1320         1437          426           NA          242          852 
TCGA-A1-A0SP TCGA-A2-A04R TCGA-A2-A0CT TCGA-A2-A0EN TCGA-A2-A0EU TCGA-A2-A0ST 
         583         2364         1917         2515          733         1643 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
        1351           NA           NA         1288         1154          337 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
         322           NA          395          321          344          397 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH 
         643          550          252          289          404          379 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT 
         358          326          334          268          661           NA 
TCGA-A7-A0D9 TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A8-A075 TCGA-A8-A08O 
         159          267          287          196          517          942 
TCGA-A8-A0A6 TCGA-A8-A0AD TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
         640         1157           10           10          375            9 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
          10           10           10           10          162          170 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03U TCGA-AO-A0JA TCGA-AO-A0JB 
        2442         1455         1645           NA          346         1150 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
        1547         1813         1965          354          449         1172 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
        1512         1319         1826         3119         3018         2850 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12C TCGA-AO-A12E TCGA-AO-A12G 
        2877         2923         2359         1993         1742         1265 
TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TT 
         439         3344         2392         1500           NA         1679 
TCGA-AR-A0TU TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U0 
         360          904          739           15         1313            8 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
          NA         2263         1627         1881         1604         1558 
TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR 
        1485         1329         1324         1215         1309           NA 
TCGA-AR-A1AS TCGA-AR-A1AT TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
        1242           NA         1409         1295         1072         1103 
TCGA-AR-A1AY TCGA-B6-A0IK TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RL 
         614           NA         6434         2082         6795           NA 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RS TCGA-B6-A0RT 
          NA         5261         4928           NA           NA         2721 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
        3991         4788         5396           NA          546           NA 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
          NA         3941         5671           NA           NA           NA 
TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B8 
         746          622          867         1203         1471         1569 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM 
        1572         1132          974          781          660         1117 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0DD 
        1640         1386         1492         1270         1464         1393 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DP TCGA-BH-A0DQ 
         713         1156          673          423          476           98 
TCGA-BH-A0DS TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0GY TCGA-BH-A0GZ 
          77          133          477          376          917          328 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
         461         1149          747          701         1247          856 
TCGA-BH-A0HB TCGA-BH-A0HF TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HP TCGA-BH-A0HX 
         806          727          619          178          414          829 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0WA 
         867          170          180          175          543          372 
TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1F0 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HL TCGA-C8-A1HM 
          NA           NA           NA            2            2            6 
TCGA-C8-A1HN TCGA-E2-A105 TCGA-E2-A106 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
           2         1163         1555          763          124         1172 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A15I 
         748          853          418          360         1350          411 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
         463           34         1964         1271         1361          911 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-A6-2672 TCGA-AK-3440 
         774          338          297          317          503         1744 
TCGA-AK-3453 TCGA-18-3417 TCGA-22-4599 TCGA-22-4601 TCGA-22-4613 TCGA-33-4566 
        1190          758         1161         1057          358         5286 
TCGA-33-4582 TCGA-33-4589 TCGA-34-5240 TCGA-34-5241 TCGA-39-5011 TCGA-39-5016 
        3149          334          235          428         1454         2253 
TCGA-39-5021 TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
        2086          740           59         1107          474         1084 
TCGA-39-5037 TCGA-63-5128 TCGA-63-5131 TCGA-AG-A026 
          24           NA           NA           59 
Variable 1:'AGE':	nDistinctValues=54,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=193,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=35,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'EXAMINATIONS.EXAMINATION.KARNOFSKYPERFORMANCESCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'HISTOLOGICAL.TYPE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.GRADE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'PATHOLOGY.T':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'PATHOLOGY.N':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'PATHOLOGICSPREAD(M)':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'TUMOR.STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'PATIENTTUMORRECURRENCESTATUS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'DAYSTOTUMORRECURRENCE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 21:'CHEMOTHERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'NUMBERPACKYEARSSMOKED':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 24:'STOPPEDSMOKINGYEAR':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 25:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 26:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 27:'BATCH.NUMBER':	nDistinctValues=17,	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] "TUMOR.STAGE"                           
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "NUMBERPACKYEARSSMOKED"                 
[10] "STOPPEDSMOKINGYEAR"                    
[11] "TOBACCOSMOKINGHISTORYINDICATOR"        
[12] "YEAROFTOBACCOSMOKINGONSET"             
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
 1  2  3  4 
11  8  4  1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "5"          
[1] "PATHOLOGY.N" "6"          
Output Data has 238 columns, 1 survival variables, and 12 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
LGALS4 
  7400 
AGE, nv=54, binary=FALSE, numeric=TRUE
FAM123C 
   4653 
PRIMARY.SITE.OF.DISEASE, nv=5, binary=FALSE, numeric=FALSE
ZNF416 
 15221 
GENDER, nv=2, binary=FALSE, numeric=FALSE
CDKL2 
 2728 
HISTOLOGICAL.TYPE, nv=5, binary=FALSE, numeric=FALSE
ZNF419 
 15224 
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
FAM89B 
  4756 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
T1 T2 T3 T4 
 7 13  2  2 
PATHOLOGY.N, nv=3, binary=FALSE, numeric=TRUE
FAM90A1 
   4758 
[1] "PATHOLOGY.N"
[1] "num to class table"
vv1
N0 N1 N2 
13  7  2 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
PRKAG1 
 10584 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
     11       8       4       1 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
DEPDC4 
  3797 
NUMBERPACKYEARSSMOKED, nv=16, binary=FALSE, numeric=TRUE
FGF22 
 4926 
STOPPEDSMOKINGYEAR, nv=13, binary=FALSE, numeric=TRUE
KIR3DL3 
   7071 
TOBACCOSMOKINGHISTORYINDICATOR, nv=3, binary=FALSE, numeric=FALSE
 TBX5 
13349 
YEAROFTOBACCOSMOKINGONSET, nv=11, binary=FALSE, numeric=TRUE
PDK2 
9882 
> q(save="no")
