
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/miRseq_preprocessor/LUAD-TP/3140810/0.miRseq_preprocessor.Finished/LUAD-TP.miRseq_RPKM_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LUAD-TP/3132696/1.GDAC_clinicalDataPicker.Finished/LUAD-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=395, in expression file=470, common to both=386
Number of genes in original expression dataset=528
[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 386 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-05-4244 TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 
          NA         1158          121          606          426           NA 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 
        1126           NA          303           NA         1431           NA 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 
          NA          610           NA           90          454           NA 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
         911           NA          913           NA          791          791 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
         761          761          730          457           31          151 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
          90           NA           30           62           14          224 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
         181          264         1448         2595         1147         1491 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
         863         1073          354         1357          158           NA 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
         133          574          581          400          529          103 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
         480          400           97          246          311          253 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
         196          189          140          106          498          208 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
           9          102          302          236           95          165 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
          82         1938           NA         1110           NA          298 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
         162          153           50          557           NA          531 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A 
         535          418          259           98          255          202 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
         246          135          114           76         2318           NA 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
          NA           NA         1081         1421          428          999 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
         268          896           NA         1314          457          369 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
         395          150            1           NA           NA         2174 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
        1485          455          785          297         1499          245 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
         282          267         1091         2369          653          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-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        1178         1479         1374           87            2          992 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
          24           NA         1238           NA           28         1475 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
          NA           NA           67           NA           NA         1826 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
          NA         1233         2161         1170           61           18 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 
          34           NA            4           95           40           39 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
          31           31           24           54           31           19 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-8087 TCGA-55-8089 
          16          197           21            3           21           92 
TCGA-55-8090 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8299 TCGA-55-8301 
           6           26            4           15          215           43 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 
         227            9            3          146          212           15 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
          48           49           65          105           33           31 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
          29           48           NA            1           28            5 
TCGA-55-A4DG TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P TCGA-62-A470 TCGA-62-A472 
         161         2093           NA           NA           NA          540 
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-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
        2550            3          926          507         1202          223 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 
          30           60           18           62           18           NA 
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-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
         414          129          230          184           70           89 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 
         382           99           76          128           61         1599 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 
         711          911           40          122          621          519 
TCGA-75-5122 TCGA-75-5125 TCGA-75-5126 TCGA-75-5146 TCGA-75-5147 TCGA-75-6203 
          NA           NA           NA           NA           NA           NA 
TCGA-75-6205 TCGA-75-6206 TCGA-75-6207 TCGA-75-6211 TCGA-75-6212 TCGA-75-6214 
          NA           NA           NA           NA           NA           NA 
TCGA-75-7025 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-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
          NA           NA           NA           NA          327          881 
TCGA-78-7542 TCGA-78-7633 TCGA-80-5607 TCGA-80-5608 TCGA-80-5611 TCGA-83-5908 
          NA          994           NA           NA           NA          420 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
          NA           NA           11           27            7           NA 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
          34           NA           14           19           10           NA 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
          13           24           43           26           23           21 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
          16           NA           19           26           34           44 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
          33           17           15           NA           NA           10 
TCGA-86-A4D0 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
          30           39           37           NA            1           39 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
          35           11           NA          819          127           28 
TCGA-91-7771 TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 
          31          297          127          185           34            2 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-97-7546 TCGA-97-7547 
         163           21           40          132          963         1435 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
        1476         1331          263          181           NA           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-97-8179 TCGA-99-7458 
         106          181           NA          146           15          250 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
         427          458           44          169          153          113 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
         287          282          238          212           76          116 
TCGA-L9-A444 TCGA-MN-A4N4 
           6          621 
Variable 1:'AGE':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=83,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=222,	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=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=69,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'PATHOLOGY.T':	nDistinctValues=9,	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=85,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=19,	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 
148  59  58  15 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "5"          
[1] "PATHOLOGY.N" "6"          
Output Data has 386 columns, 1 survival variables, and 13 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
HSA-MIR-181C 
         123 
AGE, nv=48, binary=FALSE, numeric=TRUE
HSA-MIR-29C 
        209 
GENDER, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-105-2 
           19 
KARNOFSKY.PERFORMANCE.SCORE, nv=6, binary=FALSE, numeric=TRUE
HSA-MIR-3690 
         319 
HISTOLOGICAL.TYPE, nv=12, binary=FALSE, numeric=FALSE
HSA-MIR-194-1 
          143 
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
HSA-MIR-374B 
         324 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
 T1  T2  T3  T4 
 79 165  23  16 
PATHOLOGY.N, nv=4, binary=FALSE, numeric=TRUE
HSA-MIR-200B 
         158 
[1] "PATHOLOGY.N"
[1] "num to class table"
vv1
 N0  N1  N2  N3 
169  57  51   1 
PATHOLOGICSPREAD(M), nv=3, binary=FALSE, numeric=FALSE
HSA-MIR-628 
        467 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
HSA-MIR-519A-2 
           415 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
    148      59      58      15 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-1229 
          33 
NUMBERPACKYEARSSMOKED, nv=85, binary=FALSE, numeric=TRUE
HSA-MIR-210 
        168 
TOBACCOSMOKINGHISTORYINDICATOR, nv=4, binary=FALSE, numeric=FALSE
HSA-MIR-1-2 
         12 
YEAROFTOBACCOSMOKINGONSET, nv=55, binary=FALSE, numeric=TRUE
HSA-MIR-548F-1 
           426 
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
HSA-MIR-34B 
        281 
> q(save="no")
