
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/KIRC/1676684/0.miRseq_preprocessor.Finished/KIRC.miRseq_RPKM_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/KIRC/1669679/1.GDAC_clinicalDataPicker.Finished/KIRC.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=502, in expression file=463, common to both=463
Number of genes in original expression dataset=467
[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] "NEOADJUVANTTHERAPY"                    
[18] "BATCHNUMBER"                           

Input Data has 18 rows and 463 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1436           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-A3-3331 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
        1485          137         1097         1385          910         1425 
TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
        1307         1559          319          872         1054          776 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
         735          334         1313         1070          630          567 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3426 
         574          861          726          616         3343          884 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 
        2566         2223         2017          480         1853         2192 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
        2086         2043         1744         1423         1471         1279 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
        1217         1499         1481         1190          873          683 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
          46         1168          951          853          369           40 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
          98           43          139           77          106          866 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
         577           42          109           NA          208          182 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
          26          599            5         1337          201            3 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
         214          266         1196           18           47         1491 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
        1081          848          426          183         1229         1111 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 
         454         1463          884          307         2385         2090 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
        1238         1292          728         1638          139         1636 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
         320          313         1985         1199          792          882 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
          69         1079         2145          608         1291          222 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
         233          465          221          769          433          459 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
         333          245           67          151         1584          485 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
        1913         2763         2751         1597          927          162 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
         586          560           22           90          103           NA 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
          48           55          186          190          677           10 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
        2180         2781         1487         1852          469         1042 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5701 
         944         1135         2181         2425          375         1276 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
        1158          262         3335         2414         2592         2357 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
         957         2553         2438         1864         2324          178 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
         194           50          110           90           15          214 
TCGA-B2-5635 TCGA-B2-5636 TCGA-B2-5639 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5378 
         315          258          191          168          291          175 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
           7           38           16          141          166           11 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
           7          709          511          379          279          404 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
         255           19          226          215          181           90 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
         133           22            4           23            8          248 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
          14          194          197           15          219           14 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
        3377         2600         2881         2746         3074         2839 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4174 
         992         2946           13         2718          701         1879 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
        1955         1670         2964         1624          108          845 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
        1888         1133          645          460            2         2746 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4345 TCGA-BP-4346 
        1589         2256         1912         1666         1516         1493 
TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
        1367          969          344          375         1034          953 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
         374         2208         2324         2249          182         1343 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 
        1270         2184         1461          400         1876          329 
TCGA-BP-4771 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
         161         1842          410         1731         2080          354 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
         479         1489         1111          620         1107          334 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4962 
        1133         1124          203          211         2660         1785 
TCGA-BP-4963 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
        1834         1871          204         1745         1794          432 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4976 TCGA-BP-4977 
        1487         1501         1384          220         1632          454 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
        1412          951         1124          827          117         1044 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-5000 
         500          176         1307         1371          931          563 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
        1177         1126         1071         1092          877         1463 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
         192         2411           54         2257          932         1590 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
         293         1912         1892         1495         1165         1102 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
        1133         1132          693          406          822         1010 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
         966          714          408          748         1018          603 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
        1354          881          951           29         1820         1416 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
        1924         2227          431         2308         1998         1661 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4872 
        1617         1792          336         2554         2422         1435 
TCGA-CJ-4873 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
        2258         1955         2186         1883          993         2125 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
        1951          649         1566         1945         2085          818 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
        1520          749          841         1200         1808         1527 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
        1450         1519         1559         1792         1495         1498 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
        1530         1656         1372           92          139          572 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
        1942         2190         2429         2575          782          573 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
         678          768          551         1883         1889         2230 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
        2038            6         1855           NA           NA         1905 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
        2548           NA         1964         2799         2489          164 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5590 TCGA-CW-5591 
        2609         2226         2016         2377         1075         2270 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 
        2311         2308         2430          570          774           18 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
        1943         1787          205          445         1843         1690 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
        2830          165         1768         1668         1556           25 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
         722          561         1558         1547         1558         1515 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
        1430          330          311          662         1492         1377 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
         685           73           59          945           NA         2042 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
        1491         1629          373          435          693         1599 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
        1329         1398          909          370          355         1130 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
         723         1005          727          550          118          206 
TCGA-EU-5907 
         126 
Variable 1:'AGE':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=143,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=415,	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=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=394,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=5,	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=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'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"                 "NEOADJUVANT.THERAPY"        
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
  1   2   3   4 
221  47 119  76 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 463 columns, 1 survival variables, and 8 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
HSA-MIR-130B 
          72 
AGE, nv=58, binary=FALSE, numeric=TRUE
HSA-MIR-590 
        402 
GENDER, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-100 
         13 
KARNOFSKY.PERFORMANCE.SCORE, nv=5, binary=FALSE, numeric=TRUE
HSA-MIR-3199-2 
           229 
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "num to class table"
vv1
  0  70  80  90 100 
  2   1   3  13  16 
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
HSA-MIR-139 
         84 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
 T1  T2  T3  T4 
225  59 169  10 
PATHOLOGY.N, nv=2, binary=FALSE, numeric=TRUE
HSA-MIR-3928 
         314 
PATHOLOGICSPREAD(M), nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-193A 
         131 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
HSA-MIR-139 
         84 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
    221      47     119      76 
NEOADJUVANT.THERAPY, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-2116 
         162 
> q(save="no")
