[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: MUTATION_RATE"
[1] "dfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/KIRC-TP/5094241/KIRC-TP.patients.counts_and_rates.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=417, common to both=417
Number of genes in original expression dataset=2
[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 417 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
          16           NA         1493         1491         1130         1508 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
        1478         1106         1137           NA         1610         1385 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
        2688         1307         1559          319          873         2270 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
        2274          735         1621         1070          630          567 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 
         574          861         1993          617         3343         2223 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 
        2017          480         1853         2087         2044         1471 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
        1280         1779         1481          874           NA         1143 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
        1168          951          853           43           NA           NA 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
          NA           NA           NA           NA           NA           26 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
          NA           96           NA           NA           NA          616 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
          NA           NA           18           NA           NA           NA 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
          NA           NA          183           NA           NA           NA 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 
          NA           NA           NA           NA          665           NA 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
          NA           NA           NA           NA           NA          911 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 
          NA         1092          359          797          657           59 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
         493          554          652         1132          449         3431 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
        1487         3076           NA         1420         1727         1835 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
        2583         2741         1732         1605         1203         3668 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 
        2414         2828         3117         1459         2931         1865 
TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
        2963         1092           51          374          648          358 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
         315          656          291           NA          511          826 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
         838          762          750          777          788          700 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
         636          722          822           26          737          522 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
         505          194          434           15         1046          435 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
        3377           NA         2881         2746         3074         2839 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
          NA         3037           13         2718          701           NA 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1893         1879         1955         1625          845         1888 
TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
          NA           NA         2859           NA           NA           NA 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
          NA         1516           NA         1367          372          970 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
          NA           NA           NA          374         2208         2372 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
         182           NA           NA         2184         1462          400 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 
          NA           NA         1885         1843         1731         2080 
TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
         354           NA         1489           NA         1107           NA 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 
          NA         1124          204         1459          211         2172 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
        1935         1785         1834         1862          205         1746 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
         433         1487         1502         1384           NA         1433 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
        1632          454           NA         1014         1413           NA 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
         785         1124           NA          118         1413          501 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
         177         1371          932         1266          563         1177 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
        1126          840         1140         1071           NA           NA 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
          NA          193         2412           NA         2257          932 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
          NA          293           NA         2263         1165         1291 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
        1133         1132          693          406          822         1011 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
         967          714          408          749         1018          603 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
        1355         1063          951           29         1820         1416 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
        1924           NA           NA         2308         1998           NA 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
        1793           NA          646         1498         2423         1435 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
        2259         2283         2353         1955         2186         2014 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
        1883         1759         2125         1952           NA           NA 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
        1946         2085           NA         1521          750          841 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
          NA         1808         1528         1450         1520         1560 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
        1792         1496         1499         1531         1657           NA 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
        1373           NA           NA           NA         1943           NA 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
        2430         2575           NA           NA           NA           NA 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
         552         1883         1889         2231         2038         1855 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
          NA           NA         1906         2548           NA           NA 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
        2799         2489         2609         2017         2378         2271 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
          NA         2552         3146          774         1404           18 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
          NA         1943         1787           NA         1843         1928 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
          NA         1868         1929         1789           25           NA 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
          NA         1712         1683         1732         1683         1430 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
         330           NA          662         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-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
         370          355         2016         1729           NA          551 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
         119          206          127 
Variable 1:'AGE':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=135,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=271,	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=2,	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=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=3,	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=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
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=11,	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" "RACE"                       
[9] "ETHNICITY"                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 417 columns, 1 survival variables, and 9 non-survival variables.
[1] "changed to 10 non-survival variables adding another age variable for linear regression analysis on mutaion rate."
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=56, binary=FALSE, numeric=TRUE
AGE_mutation.rate, nv=56, binary=FALSE, numeric=TRUE
$MUTATIONRATE_NONSYNONYMOUS

Call:
lm(formula = as.numeric(i) ~ vv)

Residuals:
       Min         1Q     Median         3Q        Max 
-1.277e-06 -3.955e-07 -6.210e-08  3.532e-07  2.367e-06 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)    
(Intercept) 3.321e-07  1.461e-07   2.273   0.0235 *  
vv          1.967e-08  2.361e-09   8.330 1.19e-15 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Residual standard error: 5.823e-07 on 415 degrees of freedom
Multiple R-squared: 0.1432,	Adjusted R-squared: 0.1412 
F-statistic: 69.38 on 1 and 415 DF,  p-value: 1.194e-15 


$MUTATIONRATE_SILENT

Call:
lm(formula = as.numeric(i) ~ vv)

Residuals:
       Min         1Q     Median         3Q        Max 
-4.486e-07 -1.389e-07 -1.646e-08  1.135e-07  6.954e-07 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)    
(Intercept) 7.619e-08  4.902e-08   1.554    0.121    
vv          5.912e-09  7.922e-10   7.463 5.02e-13 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Residual standard error: 1.954e-07 on 415 degrees of freedom
Multiple R-squared: 0.1183,	Adjusted R-squared: 0.1162 
F-statistic: 55.69 on 1 and 415 DF,  p-value: 5.022e-13 


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 
202  49 160   6 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=2, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=3, binary=FALSE, numeric=TRUE
[1] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "num to class table"
vv1
  0  90 100 
  1   9  13 
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
