[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/CESC-TP/11558759/iteration1/CESC-TP.patients.counts_and_rates.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/CESC-TP/11541273/CESC-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/CESC-TP/11541273/CESC-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=250, in expression file=194, common to both=194
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] "HISTOLOGICALTYPE"                                
[14] "RADIATIONS.RADIATION.REGIMENINDICATION"          
[15] "NUMBERPACKYEARSSMOKED"                           
[16] "NUMBER.OF.LYMPH.NODES"                           
[17] "RACE"                                            
[18] "ETHNICITY"                                       
[19] "BATCHNUMBER"                                     
[20] "WEIGHT_KG_AT_DIAGNOSIS"                          
[21] "TUMOR_STATUS"                                    
[22] "TUMOR_SAMPLE_PROCUREMENT_COUNTRY"                
[23] "NEOPLASMHISTOLOGICGRADE"                         
[24] "TOBACCO_SMOKING_YEAR_STOPPED"                    
[25] "TOBACCO_SMOKING_PACK_YEARS_SMOKED"               
[26] "TOBACCO_SMOKING_HISTORY"                         
[27] "PATIENT.AGEBEGANSMOKINGINYEARS"                  
[28] "RADIATION_TREATMENT_ADJUVANT"                    
[29] "RADIATION_TOTAL_DOSE"                            
[30] "RADIATION_THERAPY_TYPE"                          
[31] "RADIATION_THERAPY_STATUS"                        
[32] "RADIATION_THERAPY_SITE"                          
[33] "RADIATION_ADJUVANT_UNITS"                        
[34] "PREGNANCIES_COUNT_TOTAL"                         
[35] "PREGNANCIES_COUNT_STILLBIRTH"                    
[36] "PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT"
[37] "PREGNANCIES_COUNT_LIVE_BIRTH"                    
[38] "PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT"
[39] "PREGNANCIES_COUNT_ECTOPIC"                       
[40] "PATIENT.CERVICALCARCINOMAPELVICEXTENSIONTEXT"    
[41] "POS_LYMPH_NODE_LOCATION"                         
[42] "MENOPAUSE_STATUS"                                
[43] "LYMPHOVASCULAR_INVOLVEMENT"                      
[44] "LYMPH_NODES_EXAMINED_HE_COUNT"                   
[45] "LYMPH_NODES_EXAMINED"                            
[46] "KERATINIZATION_SQUAMOUS_CELL"                    
[47] "INITIAL_PATHOLOGIC_DX_YEAR"                      
[48] "HYSTERECTOMY_TYPE"                               
[49] "HISTORY_HORMONAL_CONTRACEPTIVES_USE"             
[50] "HEIGHT_CM_AT_DIAGNOSIS"                          
[51] "FEDPET_OR_CT_RESULTS"                            
[52] "CORPUS_INVOLVEMENT"                              
[53] "CHEMO_CONCURRENT_TYPE"                           
[54] "CERVIX_SUV_RESULTS"                              
[55] "CAUSE_OF_DEATH"                                  
[56] "AJCC_TUMOR_PATHOLOGIC_PT"                        
[57] "AGE_AT_DIAGNOSIS"                                
[58] "STAGE_EVENT.CLINICAL_STAGE"                      

Input Data has 58 rows and 194 columns.

[1] "Batch" "19"   
[1] "Last Follow UP"
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
        1505         1735          720           NA           NA           NA 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
        1112         4385         5385         5271           NA           NA 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
          NA           NA           NA         1409          919           NA 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK 
        1756         1617           NA           NA           NA           NA 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A1MQ TCGA-C5-A2LS TCGA-C5-A2LT 
          NA           NA          109         1031         1345         2226 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
        2234         2526         2383           NA         1169           25 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
        1582          548           NA          621         5564         4694 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
          NA           NA           NA          619         4482           NA 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
        2602         1846           NA           34         1791         1544 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        1367         1218         2669         1791           NA           81 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OA TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
        3589         3609          879          699          512           NA 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
         533           NA           23          376           53           40 
TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
          19           81          397           36          441           41 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
          41          441           55          385          390            8 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
         453           45          423          457          456          455 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
         413          410          383         1398          799          202 
TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
          46           NA           NA           13           18           18 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
          44            4          489            2          123            1 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN 
          11           36           NA          721           68            3 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 
           2            3            3           NA            1          619 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
         241          211          447          602          186           37 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
         725           28           66           20           31           44 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
          48           45           25          107           41           40 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
          60           34          773           NA          632          454 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
         287         4483         4172           NA         3571         2949 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
        2394         2493          808         1106          834           NA 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
         747          652          623          474          306          156 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AV 
          NA         5957          922          243          343           NA 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MU-A51Y 
          27            2            9           25            6          422 
TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 
           1          904            2          132          474          406 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
         485          103          491          534          428          483 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
         179          190          316          596          118           NA 
TCGA-UC-A7PF TCGA-WL-A834 
          NA          549 
Variable 1:'AGE':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=38,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=137,	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=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=14,	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=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'HISTOLOGICAL.TYPE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBERPACKYEARSSMOKED':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RACE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'BATCH.NUMBER':	nDistinctValues=18,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'WEIGHT_KG_AT_DIAGNOSIS':	nDistinctValues=66,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 21:'TUMOR_STATUS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'TUMOR_SAMPLE_PROCUREMENT_COUNTRY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'NEOPLASMHISTOLOGICGRADE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 24:'TOBACCO_SMOKING_YEAR_STOPPED':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 25:'TOBACCO_SMOKING_PACK_YEARS_SMOKED':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 26:'TOBACCO_SMOKING_HISTORY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 27:'PATIENT.AGEBEGANSMOKINGINYEARS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 28:'RADIATION_TREATMENT_ADJUVANT':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 29:'RADIATION_TOTAL_DOSE':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 30:'RADIATION_THERAPY_TYPE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 31:'RADIATION_THERAPY_STATUS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 32:'RADIATION_THERAPY_SITE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 33:'RADIATION_ADJUVANT_UNITS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 34:'PREGNANCIES_COUNT_TOTAL':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 35:'PREGNANCIES_COUNT_STILLBIRTH':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 36:'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 37:'PREGNANCIES_COUNT_LIVE_BIRTH':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 38:'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 39:'PREGNANCIES_COUNT_ECTOPIC':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 40:'PATIENT.CERVICALCARCINOMAPELVICEXTENSIONTEXT':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 41:'POS_LYMPH_NODE_LOCATION':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 42:'MENOPAUSE_STATUS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 43:'LYMPHOVASCULAR_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 44:'LYMPH_NODES_EXAMINED_HE_COUNT':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 45:'LYMPH_NODES_EXAMINED':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 46:'KERATINIZATION_SQUAMOUS_CELL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 47:'INITIAL_PATHOLOGIC_DX_YEAR':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 48:'HYSTERECTOMY_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 49:'HISTORY_HORMONAL_CONTRACEPTIVES_USE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 50:'HEIGHT_CM_AT_DIAGNOSIS':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 51:'FEDPET_OR_CT_RESULTS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 52:'CORPUS_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 53:'CHEMO_CONCURRENT_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 54:'CERVIX_SUV_RESULTS':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 55:'CAUSE_OF_DEATH':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 56:'AJCC_TUMOR_PATHOLOGIC_PT':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 57:'AGE_AT_DIAGNOSIS':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 58:'STAGE_EVENT.CLINICAL_STAGE':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                             
 [2] "PATHOLOGY.T.STAGE"                               
 [3] "PATHOLOGY.N.STAGE"                               
 [4] "PATHOLOGY.M.STAGE"                               
 [5] "HISTOLOGICAL.TYPE"                               
 [6] "RADIATIONS.RADIATION.REGIMENINDICATION"          
 [7] "NUMBERPACKYEARSSMOKED"                           
 [8] "NUMBER.OF.LYMPH.NODES"                           
 [9] "RACE"                                            
[10] "ETHNICITY"                                       
[11] "WEIGHT_KG_AT_DIAGNOSIS"                          
[12] "TUMOR_STATUS"                                    
[13] "TUMOR_SAMPLE_PROCUREMENT_COUNTRY"                
[14] "NEOPLASMHISTOLOGICGRADE"                         
[15] "TOBACCO_SMOKING_YEAR_STOPPED"                    
[16] "TOBACCO_SMOKING_PACK_YEARS_SMOKED"               
[17] "TOBACCO_SMOKING_HISTORY"                         
[18] "PATIENT.AGEBEGANSMOKINGINYEARS"                  
[19] "RADIATION_TOTAL_DOSE"                            
[20] "RADIATION_THERAPY_TYPE"                          
[21] "RADIATION_THERAPY_STATUS"                        
[22] "RADIATION_THERAPY_SITE"                          
[23] "PREGNANCIES_COUNT_TOTAL"                         
[24] "PREGNANCIES_COUNT_STILLBIRTH"                    
[25] "PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT"
[26] "PREGNANCIES_COUNT_LIVE_BIRTH"                    
[27] "PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT"
[28] "PREGNANCIES_COUNT_ECTOPIC"                       
[29] "POS_LYMPH_NODE_LOCATION"                         
[30] "MENOPAUSE_STATUS"                                
[31] "LYMPHOVASCULAR_INVOLVEMENT"                      
[32] "LYMPH_NODES_EXAMINED_HE_COUNT"                   
[33] "LYMPH_NODES_EXAMINED"                            
[34] "KERATINIZATION_SQUAMOUS_CELL"                    
[35] "INITIAL_PATHOLOGIC_DX_YEAR"                      
[36] "HISTORY_HORMONAL_CONTRACEPTIVES_USE"             
[37] "HEIGHT_CM_AT_DIAGNOSIS"                          
[38] "CORPUS_INVOLVEMENT"                              
[39] "CHEMO_CONCURRENT_TYPE"                           
[40] "CERVIX_SUV_RESULTS"                              
[41] "AJCC_TUMOR_PATHOLOGIC_PT"                        
[42] "AGE_AT_DIAGNOSIS"                                
[43] "STAGE_EVENT.CLINICAL_STAGE"                      
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "2"          
[1] "PATHOLOGY.N" "3"          
Output Data has 194 columns, 1 survival variables, and 43 non-survival variables.
[1] "changed to 44 non-survival variables adding another age variable for linear regression analysis on mutaion rate."
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=57, binary=FALSE, numeric=TRUE
AGE_mutation.rate, nv=57, binary=FALSE, numeric=TRUE
$MUTATIONRATE_NONSYNONYMOUS

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

Residuals:
       Min         1Q     Median         3Q        Max 
-6.733e-06 -3.177e-06 -1.931e-06 -4.460e-07  5.245e-05 

Coefficients:
              Estimate Std. Error t value Pr(>|t|)  
(Intercept) -3.018e-07  2.161e-06  -0.140   0.8891  
vv           1.054e-07  4.403e-08   2.393   0.0177 *
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Residual standard error: 8.052e-06 on 188 degrees of freedom
  (4 observations deleted due to missingness)
Multiple R-squared: 0.02957,	Adjusted R-squared: 0.0244 
F-statistic: 5.728 on 1 and 188 DF,  p-value: 0.01768 


$MUTATIONRATE_SILENT

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

Residuals:
       Min         1Q     Median         3Q        Max 
-2.085e-06 -1.041e-06 -6.075e-07 -1.173e-07  1.570e-05 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)  
(Intercept) 2.248e-08  6.437e-07   0.035    0.972  
vv          3.129e-08  1.312e-08   2.386    0.018 *
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Residual standard error: 2.399e-06 on 188 degrees of freedom
  (4 observations deleted due to missingness)
Multiple R-squared: 0.02939,	Adjusted R-squared: 0.02422 
F-statistic: 5.692 on 1 and 188 DF,  p-value: 0.01804 


PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "PATHOLOGY.T.STAGE"
[1] "num to class table"
vv1
  1   2   3   4 
106  40   3   2 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=6, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=28, binary=FALSE, numeric=TRUE
NUMBER.OF.LYMPH.NODES, nv=10, binary=FALSE, numeric=TRUE
RACE, nv=5, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
WEIGHT_KG_AT_DIAGNOSIS, nv=66, binary=FALSE, numeric=TRUE
TUMOR_STATUS, nv=2, binary=FALSE, numeric=FALSE
TUMOR_SAMPLE_PROCUREMENT_COUNTRY, nv=5, binary=FALSE, numeric=FALSE
NEOPLASMHISTOLOGICGRADE, nv=5, binary=FALSE, numeric=FALSE
TOBACCO_SMOKING_YEAR_STOPPED, nv=18, binary=FALSE, numeric=TRUE
TOBACCO_SMOKING_PACK_YEARS_SMOKED, nv=28, binary=FALSE, numeric=TRUE
TOBACCO_SMOKING_HISTORY, nv=5, binary=FALSE, numeric=FALSE
PATIENT.AGEBEGANSMOKINGINYEARS, nv=22, binary=FALSE, numeric=TRUE
RADIATION_TOTAL_DOSE, nv=23, binary=FALSE, numeric=TRUE
RADIATION_THERAPY_TYPE, nv=5, binary=FALSE, numeric=FALSE
RADIATION_THERAPY_STATUS, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY_SITE, nv=4, binary=FALSE, numeric=FALSE
PREGNANCIES_COUNT_TOTAL, nv=14, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_STILLBIRTH, nv=3, binary=FALSE, numeric=TRUE
[1] "PREGNANCIES_COUNT_STILLBIRTH"
[1] "num to class table"
vv1
 0  1  3 
95  5  1 
PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT, nv=4, binary=FALSE, numeric=TRUE
[1] "PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT"
[1] "num to class table"
vv1
 0  1  2  3 
81 25  3  1 
PREGNANCIES_COUNT_LIVE_BIRTH, nv=10, binary=FALSE, numeric=TRUE
PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT, nv=8, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_ECTOPIC, nv=3, binary=FALSE, numeric=TRUE
[1] "PREGNANCIES_COUNT_ECTOPIC"
[1] "num to class table"
vv1
 0  1  2 
93  9  1 
POS_LYMPH_NODE_LOCATION, nv=5, binary=FALSE, numeric=FALSE
MENOPAUSE_STATUS, nv=4, binary=FALSE, numeric=FALSE
LYMPHOVASCULAR_INVOLVEMENT, nv=2, binary=FALSE, numeric=FALSE
LYMPH_NODES_EXAMINED_HE_COUNT, nv=10, binary=FALSE, numeric=TRUE
LYMPH_NODES_EXAMINED, nv=46, binary=FALSE, numeric=TRUE
KERATINIZATION_SQUAMOUS_CELL, nv=2, binary=FALSE, numeric=FALSE
INITIAL_PATHOLOGIC_DX_YEAR, nv=20, binary=FALSE, numeric=TRUE
HISTORY_HORMONAL_CONTRACEPTIVES_USE, nv=3, binary=FALSE, numeric=FALSE
HEIGHT_CM_AT_DIAGNOSIS, nv=31, binary=FALSE, numeric=TRUE
CORPUS_INVOLVEMENT, nv=2, binary=FALSE, numeric=FALSE
CHEMO_CONCURRENT_TYPE, nv=3, binary=FALSE, numeric=FALSE
CERVIX_SUV_RESULTS, nv=10, binary=FALSE, numeric=TRUE
AJCC_TUMOR_PATHOLOGIC_PT, nv=14, binary=FALSE, numeric=FALSE
AGE_AT_DIAGNOSIS, nv=57, binary=FALSE, numeric=TRUE
STAGE_EVENT.CLINICAL_STAGE, nv=16, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
