[1] "libdir: /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/ClinicalAnalysisAllGenes_new/broadinstitute.org/cancer.genome.analysis/00333/60/"
[1] "terrence_modification_tag: TRUE"
[1] "op: "
[1] "dfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/KIRC-TP/11494294/KIRC-TP.meth.by_min_clin_corr.data.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIRC-TP/11541492/KIRC-TP.merged_data.txt"
[1] "gv: ALL"
[1] "gfn: "
[1] "sfn: "
[1] "fv: ALL"
[1] "ofn: "
[1] "dx: "
[1] "cfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIRC-TP/11541492/KIRC-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=525, in expression file=319, common to both=307
Number of genes in original expression dataset=20123
[1] "ALL"
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 307 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-6D-AA2E TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
         267         2688         1307         2270         2274         1621 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ 
        1070         1993          617           NA           NA            3 
TCGA-A3-A8OX TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
          NA         3343         2223         1853         2192         2087 
TCGA-AK-3440 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3458 
        1745         1280         1779         1397          874         1168 
TCGA-AK-3460 TCGA-AK-3461 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
         951          853           NA           NA           NA           NA 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
          NA           NA           NA           NA          110           NA 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
          NA           NA           26           NA           96           NA 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
          NA           NA          616           NA           NA           18 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
          NA           NA           NA           NA           NA          183 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5080 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-5083 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
          NA           NA           NA           NA           NA          665 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
          NA          911           NA         1092          359          797 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
         657          535           59          493          554          652 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
        1132          449         2408         3431         1487         3076 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
          NA         1420         1727         1835         2583         2741 
TCGA-B0-5700 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
        1082         1732         1605         1203         3668         2414 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
        2828         3117         1459         2931         2722         1865 
TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5636 
        2963         1092          648          358          315          919 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
         417          656          507          291          175            7 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
          38           16          141          166           11            7 
TCGA-B8-4146 TCGA-B8-4153 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
         511          762          788          700          636          722 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
          36          822           26          737          522          505 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
         194          434           15         1046          435          830 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
         909          519           53          256          150          528 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4177 TCGA-BP-4760 TCGA-BP-4770 TCGA-BP-4782 
         110           24         1670         2361           NA          354 
TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4993 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
         620         1124          177           NA           NA          193 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
        2412           NA         2257          932           NA          293 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
          NA         2263         1495         1165         1291         1133 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
        1132          693          406          822         1011          967 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
         714          408          749         1018          603         1355 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4869 TCGA-CJ-4882 TCGA-CJ-4897 
        1063          951           29         2554         1883         1808 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
        1450         1520         1560         1792         1496         1499 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
        1531         1657           NA         1373           NA           NA 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
          NA         1943           NA         2430         2575           NA 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
          NA           NA           NA          552         1883         1889 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
        2231         2038           NA         1855           NA           NA 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
        1906         2548           NA           NA         2799         2489 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5590 
          NA         2609         2226         2017         2378           NA 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
        2271           NA         3222         2552         3146           NA 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
         774           18         1787         1928         2830           NA 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
        1868         1929         1789           25           NA           NA 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
        1712         1683         1732         1683         1430          330 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
          NA          662         1740         1446          685           NA 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
          59           NA          386         2439         2067         1997 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
         373           NA          693         1905         1329         1398 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
        1470          370          355         1130         2016         1729 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
          NA          551          119          206          127           NA 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
         305         1727           61          591          607          337 
TCGA-MW-A4EC 
         330 
Variable 1:'AGE':	nDistinctValues=54,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=97,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=203,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=38,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                         "NEOPLASM.DISEASESTAGE"      
 [3] "PATHOLOGY.T.STAGE"           "PATHOLOGY.N.STAGE"          
 [5] "PATHOLOGY.M.STAGE"           "GENDER"                     
 [7] "KARNOFSKY.PERFORMANCE.SCORE" "NUMBERPACKYEARSSMOKED"      
 [9] "RACE"                        "ETHNICITY"                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 307 columns, 1 survival variables, and 10 non-survival variables.
                              D                 
            "D" "Time to Death"          "Year" 
AGE, nv=54, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "PATHOLOGY.T.STAGE"
[1] "num to class table"
vv1
  1   2   3   4 
149  41 109   8 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=4, binary=FALSE, numeric=TRUE
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "num to class table"
vv1
 70  80  90 100 
  1   4  15  13 
NUMBERPACKYEARSSMOKED, nv=8, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
