
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/LUAD-TP/2844079/0.GDAC_RPPA_preprocess.Finished/LUAD-TP.rppa.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LUAD-TP/2843279/1.GDAC_clinicalDataPicker.Finished/LUAD-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=376, in expression file=237, common to both=236
Number of genes in original expression dataset=174
[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] "KARNOFSKYPERFORMANCESCORE"             
[11] "HISTOLOGICALTYPE"                      
[12] "PATHOLOGICSPREAD(PT)"                  
[13] "PATHOLOGICSPREAD(PN)"                  
[14] "PATHOLOGICSPREAD(M)"                   
[15] "TUMORSTAGE"                            
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "NUMBERPACKYEARSSMOKED"                 
[18] "TOBACCOSMOKINGHISTORYINDICATOR"        
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "COMPLETENESS.OF.RESECTION"             
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 236 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-05-4244 TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4396 TCGA-05-4397 
          NA         1158          121          426          303           NA 
TCGA-05-4398 TCGA-05-4402 TCGA-05-4405 TCGA-05-4410 TCGA-05-4417 TCGA-05-4418 
        1431           NA          610           NA          454           NA 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4434 
         911           NA          791          791          761          457 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
          31          151           90           30           62           14 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
         224          181          264         1448         2595         1147 
TCGA-38-4629 TCGA-38-6178 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2664 
         863          158          581          400          103          383 
TCGA-44-2665 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 
         400          246          311          253          392          196 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
         189          140          106          498          208            9 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         102          302          236           95          165           82 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
        1938           NA         1110           NA          298          162 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
         153           50          557           NA          531          535 
TCGA-44-7672 TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4494 TCGA-49-4501 
         418         2318           NA           NA         1081         1421 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
         428          999          268          896           NA         1314 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
         457          369          395          150            1           NA 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 
          NA         2174         1485          455          297         1499 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5936 
         245          282          267         1091         2369          257 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
         460          285          135          373          349           NA 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
          NA           NA           NA           NA           NA         1015 
TCGA-50-6673 TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 
          NA          255         1068          970          418          701 
TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 
        1178         1374           87            2           24         1238 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6978 TCGA-55-6979 TCGA-55-6981 TCGA-55-6982 
          NA           28           NA           NA           NA           NA 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7728 TCGA-55-7815 TCGA-55-7910 TCGA-55-7911 
           4           95           24           54          197           21 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
        1728          628         1189         1685         1126           NA 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2550          926          507         1202          223           60 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
          27           21          422          154          186          690 
TCGA-69-7764 TCGA-69-7765 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4670 
         414          129           61         1599          711           14 
TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 TCGA-75-5122 TCGA-75-5125 
          40          122          621          519           NA           NA 
TCGA-75-6203 TCGA-75-6205 TCGA-75-6206 TCGA-75-6207 TCGA-75-6211 TCGA-75-6212 
          NA           NA           NA           NA           NA           NA 
TCGA-75-6214 TCGA-75-7027 TCGA-75-7030 TCGA-75-7031 TCGA-78-7143 TCGA-78-7145 
          NA           NA           NA           NA           NA           NA 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
          NA           NA           NA         1093           NA         1201 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
         760           NA           NA           NA           NA         1220 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
         678          214           NA         6812           NA           NA 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
          NA           NA           NA          327          881           NA 
TCGA-78-7633 TCGA-80-5607 TCGA-80-5608 TCGA-80-5611 TCGA-83-5908 TCGA-86-6562 
         994           NA           NA           NA          420           NA 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 
          NA           11           27            7           34           NA 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
          37           NA            1           39           35           11 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-93-7348 
          NA          819          127           28           31          127 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
          34            2          163           21           40          132 
TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
         963         1476         1331          263          181           NA 
TCGA-97-7941 TCGA-99-7458 
          22          250 
Variable 1:'AGE':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=65,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=153,	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=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'PATHOLOGY.T':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'PATHOLOGY.N':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'PATHOLOGICSPREAD(M)':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TUMOR.STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBERPACKYEARSSMOKED':	nDistinctValues=65,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=49,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "GENDER"                                
 [3] "KARNOFSKY.PERFORMANCE.SCORE"           
 [4] "HISTOLOGICAL.TYPE"                     
 [5] "PATHOLOGY.T"                           
 [6] "PATHOLOGY.N"                           
 [7] "PATHOLOGICSPREAD(M)"                   
 [8] "TUMOR.STAGE"                           
 [9] "RADIATIONS.RADIATION.REGIMENINDICATION"
[10] "NUMBERPACKYEARSSMOKED"                 
[11] "TOBACCOSMOKINGHISTORYINDICATOR"        
[12] "YEAROFTOBACCOSMOKINGONSET"             
[13] "COMPLETENESS.OF.RESECTION"             
[1] "TUMOR.?STAGE" "8"           
[1] "stage2"
vv
  1   2   3   4 
122  49  49  13 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "5"          
[1] "PATHOLOGY.N" "6"          
Output Data has 236 columns, 1 survival variables, and 13 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
PAI-1|PAL-1-M-C 
            112 
AGE, nv=46, binary=FALSE, numeric=TRUE
PTGS2|COX-2-R-C 
             35 
GENDER, nv=2, binary=FALSE, numeric=FALSE
CLDN7|CLAUDIN-7-R-V 
                 45 
KARNOFSKY.PERFORMANCE.SCORE, nv=6, binary=FALSE, numeric=TRUE
XRCC5|KU80-R-C 
            83 
HISTOLOGICAL.TYPE, nv=11, binary=FALSE, numeric=FALSE
PARP1|PARP_CLEAVED-M-C 
                    99 
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
KDR|VEGFR2-R-V 
           144 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
 T1  T2  T3  T4 
 64 141  17  13 
PATHOLOGY.N, nv=4, binary=FALSE, numeric=TRUE
BCL2|BCL-2-R-C 
            23 
[1] "PATHOLOGY.N"
[1] "num to class table"
vv1
 N0  N1  N2  N3 
140  46  43   1 
PATHOLOGICSPREAD(M), nv=3, binary=FALSE, numeric=FALSE
EGFR|EGFR_PY1173-R-C 
                  56 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
PIK3R1|PI3K-P85-R-V 
                104 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
    122      49      49      13 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
EIF4EBP1|4E-BP1_PS65-R-V 
                       3 
NUMBERPACKYEARSSMOKED, nv=65, binary=FALSE, numeric=TRUE
PARK7|DJ-1-R-C 
            51 
TOBACCOSMOKINGHISTORYINDICATOR, nv=4, binary=FALSE, numeric=FALSE
EIF4EBP1|4E-BP1-R-V 
                  2 
YEAROFTOBACCOSMOKINGONSET, nv=49, binary=FALSE, numeric=TRUE
EEF2K|EEF2K-R-V 
            161 
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
YBX1|YB-1_PS102-R-V 
                151 
> q(save="no")
