
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/BLCA-TP/2587637/0.GDAC_RPPA_preprocess.Finished/BLCA-TP.rppa.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/BLCA-TP/2585709/1.GDAC_clinicalDataPicker.Finished/BLCA-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=128, in expression file=54, common to both=53
Number of genes in original expression dataset=175
[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] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "NUMBERPACKYEARSSMOKED"                 
[14] "STOPPEDSMOKINGYEAR"                    
[15] "TOBACCOSMOKINGHISTORYINDICATOR"        
[16] "DISTANT.METASTASIS"                    
[17] "LYMPH.NODE.METASTASIS"                 
[18] "NUMBER.OF.LYMPH.NODES"                 
[19] "TUMOR.STAGECODE"                       
[20] "NEOPLASM.DISEASESTAGE"                 
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 53 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
         389           NA           NA           NA          363           NA 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
          NA           NA           NA           NA           NA           NA 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-C4-A0EZ 
          NA           NA           NA           NA          179           NA 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS 
          59           88           61           NA           14           13 
TCGA-CF-A27C TCGA-CU-A0YN TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA 
          21           NA           77           NA          955          214 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
         271         3616         3056          218          178          202 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-E5-A2PC TCGA-FD-A3B3 TCGA-FD-A3B4 
          55          322           NA         1108          268          253 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
         417         1518          806          172           NA          997 
TCGA-G2-A2ES TCGA-GD-A2C5 TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
         525          234           46          204           NA 
Variable 1:'AGE':	nDistinctValues=30,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=32,	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=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'NUMBERPACKYEARSSMOKED':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'STOPPEDSMOKINGYEAR':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'DISTANT.METASTASIS':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'LYMPH.NODE.METASTASIS':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'TUMOR.STAGECODE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                            "GENDER"                        
 [3] "KARNOFSKY.PERFORMANCE.SCORE"    "NUMBERPACKYEARSSMOKED"         
 [5] "STOPPEDSMOKINGYEAR"             "TOBACCOSMOKINGHISTORYINDICATOR"
 [7] "DISTANT.METASTASIS"             "LYMPH.NODE.METASTASIS"         
 [9] "NUMBER.OF.LYMPH.NODES"          "TUMOR.STAGECODE"               
[11] "NEOPLASM.DISEASESTAGE"         
[1] "TUMOR.?STAGE" "10"          
[1] "stage2"
vv
 T1 T2A T2B  T3 T3A T3B  T4 T4A T4B 
  1   2   6  12   9   9   1   6   1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 53 columns, 1 survival variables, and 11 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
PRKCA |PKC-ALPHA_PS657-R-V 
                       106 
AGE, nv=30, binary=FALSE, numeric=TRUE
DVL3|DVL3-R-V 
           52 
GENDER, nv=2, binary=FALSE, numeric=FALSE
CDKN1A|P21-R-C 
           165 
KARNOFSKY.PERFORMANCE.SCORE, nv=5, binary=FALSE, numeric=TRUE
LCK|LCK-R-V 
         83 
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "num to class table"
vv1
40 60 70 80 90 
 1  1  1  1  7 
NUMBERPACKYEARSSMOKED, nv=16, binary=FALSE, numeric=TRUE
PAI-1|PAL-1-M-C 
            112 
STOPPEDSMOKINGYEAR, nv=18, binary=FALSE, numeric=TRUE
BIRC2 |CIAP-R-V 
            159 
TOBACCOSMOKINGHISTORYINDICATOR, nv=4, binary=FALSE, numeric=TRUE
CCND1|CYCLIN_D1-R-V 
                 48 
[1] "TOBACCOSMOKINGHISTORYINDICATOR"
[1] "num to class table"
vv1
 1  2  3  4 
14 12 14  8 
DISTANT.METASTASIS, nv=3, binary=FALSE, numeric=FALSE
MAPK8|JNK_PT183_PT185-R-V 
                       79 
LYMPH.NODE.METASTASIS, nv=5, binary=FALSE, numeric=FALSE
EIF4EBP1|4E-BP1-R-V 
                  2 
NUMBER.OF.LYMPH.NODES, nv=7, binary=FALSE, numeric=TRUE
BAK1|BAK-R-C 
          21 
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
[1] "Clinical variable TUMOR.STAGECODE has too few non-missing values, n=0"
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
BCL2L1|BCL-XL-R-V 
               25 
> q(save="no")
