
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/KIRC-TP/2172489/0.GDAC_RPPA_preprocess.Finished/KIRC-TP.rppa.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/KIRC-TP/2172441/1.GDAC_clinicalDataPicker.Finished/KIRC-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=502, in expression file=454, common to both=454
Number of genes in original expression dataset=166
[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] "BATCHNUMBER"                           

Input Data has 17 rows and 454 columns.

[1] "Batch" "17"   
[1] "Last Follow UP"
TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120           16         1190          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
        1130         1508         1477         1105         1186         1137 
TCGA-A3-3329 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3346 TCGA-A3-3347 
         706         1485          664         1043          137         1097 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 
        1385          910          561         1425         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
         872         1054          776          735          334         1313 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
        1070          630          567          574          861          726 
TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 
         616         2566         2223         2086         2043         1471 
TCGA-AK-3451 TCGA-AK-3456 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
        1481           46           98           43          139           77 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
         106          866          577           42          109           NA 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
         208          182           26          599            5         1337 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
         201            3          214          266         1196           18 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
          47         1491         1081          848          426          183 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        1229         1111          454         1463          884          307 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
        2385         2090         1238         1292          728         1638 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
         139         1636          320          313         1985         1199 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
         792          882           69         1079         2145          608 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
        1291          222          233          221          769          433 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
         459          333          245           67          151         1584 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
         485         1913         2763         2751         1597          927 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
         162          586          560           22           90          103 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
          NA           48           55          186          190          677 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
          10         2180         2781         1487         1852          469 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5700 
        1042          944         1135         2181         2425          375 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
        1276         1158          262         3335         2414         2592 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
        2357          957         2553         2438         1864         2324 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
         178          194           50          110           90           15 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5636 TCGA-B2-5639 TCGA-B2-5641 TCGA-B4-5377 
         214          315          258          191          168          291 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
         175            7           38           16          141          166 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4153 TCGA-B8-4620 
          11            7          709          511          404          226 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
         215          181           90          133           22            4 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
          23            8          248           14          194          197 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4161 TCGA-BP-4164 
          15          219           14         3377         2746          992 
TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4325 
        2946          701         2343         1893         1879         2964 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
        1624          108          845         1888         2453         1133 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4341 TCGA-BP-4342 
         645          460            2         2746         1589         2256 
TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
        1912         1666         1516         1493         1367          372 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
         969          344          375         1034          953          374 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
        2208         2324         2249          182         1343         1270 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
        2184         1461          400         1876          329          161 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 
        1884         1842          410         1731         2080         1854 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
         479         1489         1111         1107          334         1133 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
        1124          203         1459          211         2660         2172 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
        1935         1785         1834         1862         1871          204 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        1745         1794          432         1487         1501         1384 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
         220         1433         1632          454         1097         1013 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
        1412          951          785         1124          827          117 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
        1044          500          176         1307         1371          931 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
        1266          563         1177         1126          840         1140 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
        1071         1092          877         1463          192         2411 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
          54         2257          932         1590          293         1912 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        1892         1495         1165         1102         1133         1132 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
         693          406          822         1010          966          714 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
         408          748         1018          603         1354          881 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4638 TCGA-CJ-4640 
         951           29         1820         1416          431         1998 
TCGA-CJ-4642 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
        1617          645         2554         1497         2422         1435 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
        2258         2283         2353         1955         2186         2013 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
        1883          993         2125         1951          649         1566 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
        1945         2085          818         1520          749          841 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
        1200         1808         1527         1274         1450         1519 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
        1559         1792         1495         1498         1530         1656 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
        1173         1372           92          139          572         1942 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
        2190         2429         2575          782          573          678 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
         768          551         1883         1889         2230         2038 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
           6         1855           NA           NA         1905         2548 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
          NA         1964         2799         2489          164         2609 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5590 TCGA-CW-5591 TCGA-CW-6087 
        2226         2016         2377         1075         2270           41 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6096 TCGA-CW-6097 TCGA-CZ-4853 
        2311         2308         2430         2127          570          774 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
        1404           18         1432         1943         1787          205 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
         445         1843         1690         2830          165         1768 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
        1668         1556           25          722          561         1558 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
        1547         1558         1515         1430          330          311 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
         662         1492         1377          685           73           59 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
         945           NA         2042         1491         1629          373 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
         435          693         1599         1329         1398          909 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
         370          355         1130          723         1005          727 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
         550          118          206          126 
Variable 1:'AGE':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=145,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=410,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	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=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=394,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'PATHOLOGY.T':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'PATHOLOGY.N':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'PATHOLOGICSPREAD(M)':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TUMOR.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'BATCH.NUMBER':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                         "GENDER"                     
[3] "KARNOFSKY.PERFORMANCE.SCORE" "PATHOLOGY.T"                
[5] "PATHOLOGY.N"                 "PATHOLOGICSPREAD(M)"        
[7] "TUMOR.STAGE"                
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
  1   2   3   4 
219  43 114  78 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 454 columns, 1 survival variables, and 7 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
VASP|VASP-R-C 
          137 
AGE, nv=58, binary=FALSE, numeric=TRUE
IGFBP2|IGFBP2-R-V 
               76 
GENDER, nv=2, binary=FALSE, numeric=FALSE
AR|AR-R-V 
       13 
KARNOFSKY.PERFORMANCE.SCORE, nv=4, binary=FALSE, numeric=TRUE
YAP1|YAP-R-V 
         142 
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "num to class table"
vv1
 70  80  90 100 
  1   3  13  17 
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
ERBB3|HER3_PY1298-R-C 
                   73 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
 T1  T2  T3  T4 
224  54 165  11 
PATHOLOGY.N, nv=2, binary=FALSE, numeric=TRUE
EGFR|EGFR_PY1068-R-V 
                  54 
PATHOLOGICSPREAD(M), nv=2, binary=FALSE, numeric=FALSE
ERBB3|HER3_PY1298-R-C 
                   73 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
ERBB3|HER3_PY1298-R-C 
                   73 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
    219      43     114      78 
> q(save="no")
